BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472766.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,960,098 number of mapped reads = 13,816,720 (98.97%) number of supplementary alignments = 49,312 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,936,867 number of mapped paired reads (second in pair) = 6,879,853 number of mapped paired reads (both in pair) = 13,727,772 number of mapped paired reads (singletons) = 88,948 number of mapped bases = 1,363,499,908 bp number of sequenced bases = 1,363,314,090 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,458,992 duplication rate = 46.54% >>>>>>> Insert size mean insert size = 21,286.5536 std insert size = 1,420,020.3189 median insert size = 262 >>>>>>> Mapping quality mean mapping quality = 55.1388 >>>>>>> ACTG content number of A's = 382,510,470 bp (28.06%) number of C's = 301,097,713 bp (22.09%) number of T's = 380,700,683 bp (27.92%) number of G's = 298,745,369 bp (21.91%) number of N's = 259,855 bp (0.02%) GC percentage = 44% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 8,899,264 number of insertions = 80,927 mapped reads with insertion percentage = 0.58% number of deletions = 77,350 mapped reads with deletion percentage = 0.55% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.4405X std coverageData = 16.2257X There is a 3.95% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 150617701 0.604282149411375 28.72859309727247 chr2 243199373 84782658 0.3486138017304839 11.164407201587382 chr3 198022430 171222749 0.8646634070695931 20.86723072582451 chr4 191154276 63783923 0.33367772008406443 16.75515010280963 chr5 180915260 71492757 0.39517261838498313 12.874569521225904 chr6 171115067 94496782 0.552241153609226 15.197548683525532 chr7 159138663 50362144 0.3164670548979037 10.477049925250046 chr8 146364022 56944150 0.38905838485362204 13.483913608606162 chr9 141213431 92920540 0.6580148881164144 16.776175292613534 chr10 135534747 42738589 0.31533307838764035 12.868336360599539 chr11 135006516 62448343 0.462557992386086 15.3309073677768 chr12 133851895 65384800 0.48848617346807083 16.286758043197175 chr13 115169878 25851714 0.22446593196877399 8.195390364640895 chr14 107349540 37132018 0.34589824977359007 12.624215481016476 chr15 102531392 40341769 0.3934577324376909 13.817857696588836 chr16 90354753 43235523 0.47850856279801907 12.510561900341791 chr17 81195210 47091570 0.5799796564353981 13.989608054517133 chr18 78077248 27231451 0.34877575346917966 17.461564409022962 chr19 59128983 28710394 0.48555534939608214 27.191296655476158 chr20 63025520 42026979 0.6668247878002435 24.293913716672918 chr21 48129895 8034690 0.1669376174620784 8.596984804714586 chr22 51304566 9979017 0.19450543641671192 6.440458008892167 chrMT 16571 4444 0.26817934946593447 1.0142096960727327 chrX 155270560 42015833 0.27059754920701 7.967539383989397 chrY 59373566 4649370 0.07830707018675617 4.6294902981480694