BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514741.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 36,090,679 number of mapped reads = 34,170,549 (94.68%) number of supplementary alignments = 1,368,022 (3.79%) number of secondary alignments = 0 number of mapped bases = 3,187,188,980 bp number of sequenced bases = 3,183,688,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,561,963 duplication rate = 35.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.8865 >>>>>>> ACTG content number of A's = 820,199,401 bp (25.76%) number of C's = 756,637,866 bp (23.77%) number of T's = 826,870,423 bp (25.97%) number of G's = 759,209,010 bp (23.85%) number of N's = 20,772,017 bp (0.65%) GC percentage = 47.61% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 36,081,205 number of insertions = 1,489,080 mapped reads with insertion percentage = 4.08% number of deletions = 1,225,586 mapped reads with deletion percentage = 3.39% homopolymer indels = 37.97% >>>>>>> Coverage mean coverageData = 1.0296X std coverageData = 40.0592X There is a 7.86% of reference with a coverageData >= 1X There is a 4.16% of reference with a coverageData >= 2X There is a 2.78% of reference with a coverageData >= 3X There is a 2.17% of reference with a coverageData >= 4X There is a 1.82% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 1.43% of reference with a coverageData >= 7X There is a 1.31% of reference with a coverageData >= 8X There is a 1.22% of reference with a coverageData >= 9X There is a 1.14% of reference with a coverageData >= 10X There is a 1.08% of reference with a coverageData >= 11X There is a 1.02% of reference with a coverageData >= 12X There is a 0.97% of reference with a coverageData >= 13X There is a 0.93% of reference with a coverageData >= 14X There is a 0.89% of reference with a coverageData >= 15X There is a 0.86% of reference with a coverageData >= 16X There is a 0.83% of reference with a coverageData >= 17X There is a 0.8% of reference with a coverageData >= 18X There is a 0.77% of reference with a coverageData >= 19X There is a 0.75% of reference with a coverageData >= 20X There is a 0.73% of reference with a coverageData >= 21X There is a 0.71% of reference with a coverageData >= 22X There is a 0.69% of reference with a coverageData >= 23X There is a 0.67% of reference with a coverageData >= 24X There is a 0.65% of reference with a coverageData >= 25X There is a 0.63% of reference with a coverageData >= 26X There is a 0.62% of reference with a coverageData >= 27X There is a 0.6% of reference with a coverageData >= 28X There is a 0.59% of reference with a coverageData >= 29X There is a 0.58% of reference with a coverageData >= 30X There is a 0.56% of reference with a coverageData >= 31X There is a 0.55% of reference with a coverageData >= 32X There is a 0.54% of reference with a coverageData >= 33X There is a 0.53% of reference with a coverageData >= 34X There is a 0.52% of reference with a coverageData >= 35X There is a 0.51% of reference with a coverageData >= 36X There is a 0.5% of reference with a coverageData >= 37X There is a 0.49% of reference with a coverageData >= 38X There is a 0.48% of reference with a coverageData >= 39X There is a 0.47% of reference with a coverageData >= 40X There is a 0.46% of reference with a coverageData >= 41X There is a 0.45% of reference with a coverageData >= 42X There is a 0.45% of reference with a coverageData >= 43X There is a 0.44% of reference with a coverageData >= 44X There is a 0.43% of reference with a coverageData >= 45X There is a 0.42% of reference with a coverageData >= 46X There is a 0.42% of reference with a coverageData >= 47X There is a 0.41% of reference with a coverageData >= 48X There is a 0.4% of reference with a coverageData >= 49X There is a 0.4% of reference with a coverageData >= 50X There is a 0.39% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 394111390 1.5811851878996923 22.950672464081357 chr2 243199373 284667648 1.1705114387774347 101.08315820676503 chr3 198022430 205329964 1.0369025569477155 20.46008128384472 chr4 191154276 98048490 0.512928572939692 20.018498495462577 chr5 180915260 156760896 0.8664879679027628 21.203489390007707 chr6 171115067 193082995 1.1283810267859113 25.256480342857767 chr7 159138663 91698139 0.5762153412084403 13.505240294464906 chr8 146364022 160915668 1.0994209218984157 18.736544615260506 chr9 141213431 87599176 0.6203317586696127 19.22000576677707 chr10 135534747 116893793 0.8624636529553562 64.89722157304219 chr11 135006516 100746398 0.746233596606552 17.30380624982641 chr12 133851895 182449575 1.3630705415115714 17.47970614335645 chr13 115169878 88474292 0.7682068743703975 15.132405800859953 chr14 107349540 111720814 1.040720006811394 23.753839307056566 chr15 102531392 61733153 0.6020902651940978 11.337883434633703 chr16 90354753 145487057 1.610176024718921 68.76454134817925 chr17 81195210 228224427 2.8108114628929464 37.23561856833657 chr18 78077248 54234606 0.6946275309293688 40.16109088225735 chr19 59128983 189105792 3.198191181471868 35.16562530758314 chr20 63025520 86784886 1.3769800867965865 18.365163399140954 chr21 48129895 23475071 0.4877440725769296 12.119225910047064 chr22 51304566 67974476 1.3249205928376824 18.82931860858965 chrMT 16571 5862226 353.76416631464605 186.87334861537883 chrX 155270560 21783524 0.14029397459505524 10.187844997526764 chrY 59373566 30024524 0.5056884068576916 72.43887053359182