BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671991.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 22,220,828 number of mapped reads = 22,110,996 (99.51%) number of supplementary alignments = 92,295 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,058,222 number of mapped paired reads (second in pair) = 11,052,774 number of mapped paired reads (both in pair) = 22,090,252 number of mapped paired reads (singletons) = 20,744 number of mapped bases = 3,026,698,120 bp number of sequenced bases = 3,025,623,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,136,693 duplication rate = 56.65% >>>>>>> Insert size mean insert size = 34,565.706 std insert size = 1,777,619.5333 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 53.0008 >>>>>>> ACTG content number of A's = 762,505,620 bp (25.2%) number of C's = 698,225,102 bp (23.08%) number of T's = 795,911,931 bp (26.31%) number of G's = 768,972,123 bp (25.42%) number of N's = 8,424 bp (0%) GC percentage = 48.49% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 22,647,816 number of insertions = 201,305 mapped reads with insertion percentage = 0.89% number of deletions = 588,477 mapped reads with deletion percentage = 2.61% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.9777X std coverageData = 69.0349X There is a 4.3% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.1% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175504134 0.704127168453474 50.92173853678114 chr2 243199373 306114623 1.2586982409695604 81.23283464211805 chr3 198022430 20576032 0.10390758259051765 5.554331260154169 chr4 191154276 202429464 1.0589847542829751 72.37382926090497 chr5 180915260 85203894 0.47096023851166563 44.08126443703211 chr6 171115067 159281521 0.9308445117810695 69.48936977380367 chr7 159138663 163718826 1.0287809568941773 79.16747525306735 chr8 146364022 14386882 0.09829520809424054 1.0570628335868306 chr9 141213431 144774082 1.0252146766407793 73.67327091676115 chr10 135534747 127892011 0.943610504544639 55.601838512654034 chr11 135006516 239488452 1.7739029129527348 88.41422977497075 chr12 133851895 167237296 1.2494204583356852 91.42092004199397 chr13 115169878 133110708 1.155777103454082 89.61213938927199 chr14 107349540 76605529 0.7136083582659041 55.14374873471572 chr15 102531392 100770648 0.9828272691352907 61.85268727852991 chr16 90354753 125725462 1.3914648408147383 61.08962729103324 chr17 81195210 206914786 2.5483619784960223 107.24968065429856 chr18 78077248 9315564 0.11931214583792707 4.884784046884551 chr19 59128983 32116675 0.5431629865847685 45.11251722695732 chr20 63025520 54729344 0.8683679880784799 67.0498121315885 chr21 48129895 34442821 0.715622192817998 57.9729782098306 chr22 51304566 3938136 0.07675995154115522 6.050518014631384 chrMT 16571 7115 0.429364552531531 1.3094706904552762 chrX 155270560 437109854 2.815149594359678 126.03515360855737 chrY 59373566 5304261 0.08933707973679735 11.908170642959506