BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432712.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 335,190,218 number of mapped reads = 335,047,863 (99.96%) number of supplementary alignments = 1,168,997 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 167,528,607 number of mapped paired reads (second in pair) = 167,519,256 number of mapped paired reads (both in pair) = 334,994,926 number of mapped paired reads (singletons) = 52,937 number of mapped bases = 47,577,821,903 bp number of sequenced bases = 47,529,052,539 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,969,732 duplication rate = 35.3% >>>>>>> Insert size mean insert size = 36,211.57 std insert size = 1,942,560.1268 median insert size = 330 >>>>>>> Mapping quality mean mapping quality = 57.4785 >>>>>>> ACTG content number of A's = 13,282,893,622 bp (27.95%) number of C's = 10,131,272,864 bp (21.32%) number of T's = 13,120,911,023 bp (27.61%) number of G's = 10,987,938,393 bp (23.12%) number of N's = 6,036,637 bp (0.01%) GC percentage = 44.43% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 416,639,811 number of insertions = 10,181,639 mapped reads with insertion percentage = 2.97% number of deletions = 34,972,577 mapped reads with deletion percentage = 9.91% homopolymer indels = 53.7% >>>>>>> Coverage mean coverageData = 15.369X std coverageData = 54.9752X There is a 32.24% of reference with a coverageData >= 1X There is a 29.4% of reference with a coverageData >= 2X There is a 27.54% of reference with a coverageData >= 3X There is a 26.07% of reference with a coverageData >= 4X There is a 24.82% of reference with a coverageData >= 5X There is a 23.71% of reference with a coverageData >= 6X There is a 22.71% of reference with a coverageData >= 7X There is a 21.8% of reference with a coverageData >= 8X There is a 20.97% of reference with a coverageData >= 9X There is a 20.2% of reference with a coverageData >= 10X There is a 19.49% of reference with a coverageData >= 11X There is a 18.83% of reference with a coverageData >= 12X There is a 18.22% of reference with a coverageData >= 13X There is a 17.65% of reference with a coverageData >= 14X There is a 17.12% of reference with a coverageData >= 15X There is a 16.62% of reference with a coverageData >= 16X There is a 16.15% of reference with a coverageData >= 17X There is a 15.71% of reference with a coverageData >= 18X There is a 15.3% of reference with a coverageData >= 19X There is a 14.9% of reference with a coverageData >= 20X There is a 14.53% of reference with a coverageData >= 21X There is a 14.17% of reference with a coverageData >= 22X There is a 13.83% of reference with a coverageData >= 23X There is a 13.51% of reference with a coverageData >= 24X There is a 13.2% of reference with a coverageData >= 25X There is a 12.9% of reference with a coverageData >= 26X There is a 12.62% of reference with a coverageData >= 27X There is a 12.35% of reference with a coverageData >= 28X There is a 12.08% of reference with a coverageData >= 29X There is a 11.83% of reference with a coverageData >= 30X There is a 11.59% of reference with a coverageData >= 31X There is a 11.36% of reference with a coverageData >= 32X There is a 11.13% of reference with a coverageData >= 33X There is a 10.91% of reference with a coverageData >= 34X There is a 10.7% of reference with a coverageData >= 35X There is a 10.5% of reference with a coverageData >= 36X There is a 10.3% of reference with a coverageData >= 37X There is a 10.11% of reference with a coverageData >= 38X There is a 9.93% of reference with a coverageData >= 39X There is a 9.75% of reference with a coverageData >= 40X There is a 9.58% of reference with a coverageData >= 41X There is a 9.41% of reference with a coverageData >= 42X There is a 9.25% of reference with a coverageData >= 43X There is a 9.09% of reference with a coverageData >= 44X There is a 8.94% of reference with a coverageData >= 45X There is a 8.79% of reference with a coverageData >= 46X There is a 8.64% of reference with a coverageData >= 47X There is a 8.5% of reference with a coverageData >= 48X There is a 8.36% of reference with a coverageData >= 49X There is a 8.23% of reference with a coverageData >= 50X There is a 8.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5097448633 20.451097022542623 65.62883013554676 chr2 243199373 3254356814 13.381435872369622 51.7114579518651 chr3 198022430 3475469913 17.550890134011585 55.72543240973961 chr4 191154276 1914966372 10.017910203588645 38.98463047635752 chr5 180915260 2511832872 13.884029860167683 48.753148859914035 chr6 171115067 1830302898 10.696328091318808 44.42079498981235 chr7 159138663 1858058448 11.675719859478773 44.55051219528939 chr8 146364022 1963000550 13.41176966290254 46.92092174294741 chr9 141213431 2359974859 16.71211330457653 59.4490793247354 chr10 135534747 2403998556 17.737138329553233 57.73481500043132 chr11 135006516 1943541605 14.395909638909577 51.11644449289061 chr12 133851895 3294022941 24.609460635577854 71.99807676445259 chr13 115169878 1212071367 10.524204662264207 42.88966938578509 chr14 107349540 2088003382 19.450510752072155 63.21869306372491 chr15 102531392 1791141264 17.469198740615948 61.05558757029152 chr16 90354753 1572183838 17.400123245315054 67.43688035083692 chr17 81195210 2047273587 25.214216294286327 72.82813478734326 chr18 78077248 1708071405 21.87668557426614 67.35743930440148 chr19 59128983 1253317206 21.196326106268394 68.01158713474476 chr20 63025520 1116323939 17.71225273508255 58.92420594876745 chr21 48129895 718389067 14.926046836378928 54.16899732307348 chr22 51304566 847661442 16.522144286338957 59.147176351522 chrMT 16571 5258213 317.3141632973267 483.2808750899851 chrX 155270560 1151897063 7.4186443521553604 33.65450429957051 chrY 59373566 159255669 2.682265522000144 25.596731213344142