BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438282.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 640,533,988 number of mapped reads = 638,512,766 (99.68%) number of supplementary alignments = 11,179,827 (1.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 319,480,812 number of mapped paired reads (second in pair) = 319,031,954 number of mapped paired reads (both in pair) = 637,092,372 number of mapped paired reads (singletons) = 1,420,394 number of mapped bases = 91,714,343,672 bp number of sequenced bases = 91,690,507,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,380,889 duplication rate = 30.41% >>>>>>> Insert size mean insert size = 38,166.8795 std insert size = 1,909,169.2533 median insert size = 265 >>>>>>> Mapping quality mean mapping quality = 55.2266 >>>>>>> ACTG content number of A's = 27,603,725,798 bp (30.11%) number of C's = 18,468,555,622 bp (20.14%) number of T's = 26,298,858,766 bp (28.68%) number of G's = 19,318,678,165 bp (21.07%) number of N's = 688,912 bp (0%) GC percentage = 41.21% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 468,591,438 number of insertions = 10,852,469 mapped reads with insertion percentage = 1.67% number of deletions = 9,586,568 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 29.6264X std coverageData = 38.7346X There is a 91.64% of reference with a coverageData >= 1X There is a 90.98% of reference with a coverageData >= 2X There is a 90.19% of reference with a coverageData >= 3X There is a 89.27% of reference with a coverageData >= 4X There is a 88.22% of reference with a coverageData >= 5X There is a 87.03% of reference with a coverageData >= 6X There is a 85.7% of reference with a coverageData >= 7X There is a 84.25% of reference with a coverageData >= 8X There is a 82.68% of reference with a coverageData >= 9X There is a 81.01% of reference with a coverageData >= 10X There is a 79.24% of reference with a coverageData >= 11X There is a 77.39% of reference with a coverageData >= 12X There is a 75.47% of reference with a coverageData >= 13X There is a 73.5% of reference with a coverageData >= 14X There is a 71.47% of reference with a coverageData >= 15X There is a 69.42% of reference with a coverageData >= 16X There is a 67.33% of reference with a coverageData >= 17X There is a 65.23% of reference with a coverageData >= 18X There is a 63.13% of reference with a coverageData >= 19X There is a 61.03% of reference with a coverageData >= 20X There is a 58.93% of reference with a coverageData >= 21X There is a 56.86% of reference with a coverageData >= 22X There is a 54.81% of reference with a coverageData >= 23X There is a 52.79% of reference with a coverageData >= 24X There is a 50.8% of reference with a coverageData >= 25X There is a 48.85% of reference with a coverageData >= 26X There is a 46.94% of reference with a coverageData >= 27X There is a 45.07% of reference with a coverageData >= 28X There is a 43.26% of reference with a coverageData >= 29X There is a 41.49% of reference with a coverageData >= 30X There is a 39.77% of reference with a coverageData >= 31X There is a 38.1% of reference with a coverageData >= 32X There is a 36.48% of reference with a coverageData >= 33X There is a 34.92% of reference with a coverageData >= 34X There is a 33.41% of reference with a coverageData >= 35X There is a 31.95% of reference with a coverageData >= 36X There is a 30.55% of reference with a coverageData >= 37X There is a 29.2% of reference with a coverageData >= 38X There is a 27.89% of reference with a coverageData >= 39X There is a 26.64% of reference with a coverageData >= 40X There is a 25.44% of reference with a coverageData >= 41X There is a 24.28% of reference with a coverageData >= 42X There is a 23.18% of reference with a coverageData >= 43X There is a 22.11% of reference with a coverageData >= 44X There is a 21.1% of reference with a coverageData >= 45X There is a 20.12% of reference with a coverageData >= 46X There is a 19.19% of reference with a coverageData >= 47X There is a 18.29% of reference with a coverageData >= 48X There is a 17.44% of reference with a coverageData >= 49X There is a 16.63% of reference with a coverageData >= 50X There is a 15.85% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7761923322 31.141039050811433 26.976071326836653 chr2 243199373 8196112824 33.701208695139194 87.31753111236743 chr3 198022430 6486623857 32.757015743115566 23.88164550535591 chr4 191154276 5881877171 30.770314397779938 22.342495405118974 chr5 180915260 5970313582 33.00060803052214 23.432523079295112 chr6 171115067 5700929254 33.31634878184047 24.58723797034209 chr7 159138663 5062724827 31.81329245552352 23.349048804526955 chr8 146364022 4827720508 32.98433892449334 24.56916821648065 chr9 141213431 4042761036 28.628728920268216 28.060568173439275 chr10 135534747 4555407333 33.610623355500124 26.740862699508057 chr11 135006516 4242902984 31.42739409703751 24.44596218004665 chr12 133851895 4359492811 32.56952627379687 23.425761213164634 chr13 115169878 3057044985 26.54378938388734 23.925058730381505 chr14 107349540 2847551795 26.525980409417684 24.541186929442784 chr15 102531392 2789133278 27.20272517123341 26.4611919969967 chr16 90354753 2481325437 27.462035527893036 36.19458330844443 chr17 81195210 2224550556 27.397558993935725 29.77443904904583 chr18 78077248 2439458650 31.24416795530498 24.251668934656596 chr19 59128983 1422212637 24.052716025912368 25.604928338458016 chr20 63025520 2101634397 33.34576846014122 26.264706958703528 chr21 48129895 1155967468 24.0176602920077 26.768865420184383 chr22 51304566 1024438791 19.96778982595818 24.990423672805054 chrMT 16571 117949262 7117.811960654155 2503.804398934013 chrX 155270560 2608661384 16.8007469284583 13.63095946266038 chrY 59373566 355625523 5.989627151584596 17.932494551399977