BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173913.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,593,744 number of mapped reads = 5,459,676 (97.6%) number of supplementary alignments = 574,251 (10.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,732,115 number of mapped paired reads (second in pair) = 2,727,561 number of mapped paired reads (both in pair) = 5,369,078 number of mapped paired reads (singletons) = 90,598 number of mapped bases = 648,253,739 bp number of sequenced bases = 647,868,930 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,376,731 duplication rate = 66.06% >>>>>>> Insert size mean insert size = 1,018,366.5781 std insert size = 9,119,547.7488 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.7291 >>>>>>> ACTG content number of A's = 194,998,893 bp (30.1%) number of C's = 126,548,092 bp (19.53%) number of T's = 194,812,419 bp (30.07%) number of G's = 131,501,793 bp (20.3%) number of N's = 7,733 bp (0%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 6,591,687 number of insertions = 66,662 mapped reads with insertion percentage = 1.18% number of deletions = 164,168 mapped reads with deletion percentage = 2.94% homopolymer indels = 42.38% >>>>>>> Coverage mean coverageData = 0.2094X std coverageData = 2.9853X There is a 4.06% of reference with a coverageData >= 1X There is a 3.25% of reference with a coverageData >= 2X There is a 2.57% of reference with a coverageData >= 3X There is a 2.15% of reference with a coverageData >= 4X There is a 1.69% of reference with a coverageData >= 5X There is a 1.39% of reference with a coverageData >= 6X There is a 1.06% of reference with a coverageData >= 7X There is a 0.87% of reference with a coverageData >= 8X There is a 0.66% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 59836111 0.24006403980032612 1.797844521037839 chr2 243199373 47384604 0.19483851218646028 8.605719527524062 chr3 198022430 40297009 0.20349719473698005 1.3565199810548165 chr4 191154276 39400464 0.2061186640679699 1.6100029250655794 chr5 180915260 33605328 0.1857517602439949 1.290877013545646 chr6 171115067 28387169 0.1658952043071695 1.2914641684831425 chr7 159138663 57533915 0.3615332309283006 3.207400307846341 chr8 146364022 62690969 0.4283222621471826 2.2917761670116645 chr9 141213431 23337309 0.16526267250032328 1.430648569859356 chr10 135534747 29945774 0.22094536392206496 3.835493727288944 chr11 135006516 26954250 0.1996514745999371 1.3525685186458078 chr12 133851895 24839484 0.18557439175590304 1.2849239012245823 chr13 115169878 16046317 0.13932737690318645 1.1141231398278957 chr14 107349540 22235269 0.20712961601884833 1.3606879341108318 chr15 102531392 15909172 0.15516391311648242 1.1631963127276588 chr16 90354753 15223046 0.1684808545710927 1.5810288746701582 chr17 81195210 16722057 0.20594881151240327 1.5013080392419893 chr18 78077248 12249998 0.15689587317421844 1.9576343077987166 chr19 59128983 8829823 0.1493315553896809 1.403593891088946 chr20 63025520 25166758 0.39931059672335906 1.9027767434070906 chr21 48129895 8288863 0.17221859719411398 1.2951879488534699 chr22 51304566 7218830 0.14070541011885765 1.0739180858157331 chrMT 16571 1500146 90.5283929756804 75.26781472055123 chrX 155270560 23565740 0.15177210670200456 1.1706874322803276 chrY 59373566 1085334 0.018279750958532622 0.7698782627888879