BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617724.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 42,378,006 number of mapped reads = 41,494,481 (97.92%) number of supplementary alignments = 1,518,404 (3.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,959,340 number of mapped paired reads (second in pair) = 20,535,141 number of mapped paired reads (both in pair) = 40,931,792 number of mapped paired reads (singletons) = 562,689 number of mapped bases = 5,494,048,352 bp number of sequenced bases = 5,489,589,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,418,748 duplication rate = 24.77% >>>>>>> Insert size mean insert size = 269,359.8295 std insert size = 5,169,050.6192 median insert size = 273 >>>>>>> Mapping quality mean mapping quality = 53.113 >>>>>>> ACTG content number of A's = 1,569,770,456 bp (28.6%) number of C's = 1,053,183,658 bp (19.19%) number of T's = 1,620,264,566 bp (29.52%) number of G's = 1,246,158,519 bp (22.7%) number of N's = 212,166 bp (0%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 64,482,872 number of insertions = 1,033,127 mapped reads with insertion percentage = 2.33% number of deletions = 2,276,676 mapped reads with deletion percentage = 5.25% homopolymer indels = 45.38% >>>>>>> Coverage mean coverageData = 1.7747X std coverageData = 15.3215X There is a 37.87% of reference with a coverageData >= 1X There is a 27.17% of reference with a coverageData >= 2X There is a 20.14% of reference with a coverageData >= 3X There is a 15.54% of reference with a coverageData >= 4X There is a 12.14% of reference with a coverageData >= 5X There is a 9.66% of reference with a coverageData >= 6X There is a 7.76% of reference with a coverageData >= 7X There is a 6.3% of reference with a coverageData >= 8X There is a 5.15% of reference with a coverageData >= 9X There is a 4.25% of reference with a coverageData >= 10X There is a 3.52% of reference with a coverageData >= 11X There is a 2.94% of reference with a coverageData >= 12X There is a 2.47% of reference with a coverageData >= 13X There is a 2.08% of reference with a coverageData >= 14X There is a 1.76% of reference with a coverageData >= 15X There is a 1.5% of reference with a coverageData >= 16X There is a 1.28% of reference with a coverageData >= 17X There is a 1.1% of reference with a coverageData >= 18X There is a 0.95% of reference with a coverageData >= 19X There is a 0.82% of reference with a coverageData >= 20X There is a 0.71% of reference with a coverageData >= 21X There is a 0.62% of reference with a coverageData >= 22X There is a 0.54% of reference with a coverageData >= 23X There is a 0.47% of reference with a coverageData >= 24X There is a 0.41% of reference with a coverageData >= 25X There is a 0.36% of reference with a coverageData >= 26X There is a 0.32% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 480230730 1.9266982287679035 9.68895462485987 chr2 243199373 543575622 2.2351028923088547 20.277428681357538 chr3 198022430 353404260 1.7846678277809236 4.098361910761628 chr4 191154276 327574193 1.713663956960084 16.210981479866522 chr5 180915260 340538931 1.8823118127238134 4.303809405183889 chr6 171115067 259042597 1.5138503086931556 6.216357421920327 chr7 159138663 311566274 1.9578289029611868 17.277926533386903 chr8 146364022 310647699 2.122432102883863 5.496038223174842 chr9 141213431 237677118 1.683105610542102 22.376178895099088 chr10 135534747 297364591 2.194010005419496 41.23043396808689 chr11 135006516 269479541 1.996048405545107 9.341066619808354 chr12 133851895 226314368 1.6907819497064274 9.025114582217581 chr13 115169878 166527616 1.4459302978509712 3.520479235094108 chr14 107349540 182146277 1.6967588030652017 4.3899795930153624 chr15 102531392 168525511 1.6436479375994426 5.2191025911251 chr16 90354753 190241425 2.1054943838981 24.383870456537817 chr17 81195210 135718107 1.6715038608804633 14.538670695225848 chr18 78077248 155074100 1.9861624733494705 20.194182353380278 chr19 59128983 103797706 1.7554454809412163 6.1207883966780985 chr20 63025520 123014537 1.951821055978594 6.371529588029108 chr21 48129895 75394085 1.5664710051829533 9.19950342252875 chr22 51304566 60604693 1.1812728909937569 4.053151932712901 chrMT 16571 3369849 203.35821616076277 110.22495010129484 chrX 155270560 151611250 0.9764326862735602 4.047359030083415 chrY 59373566 20607272 0.3470782266977193 26.45427042777572