BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525163.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,861,125 number of mapped reads = 2,592,646 (90.62%) number of supplementary alignments = 8,319 (0.29%) number of secondary alignments = 0 number of mapped bases = 149,828,916 bp number of sequenced bases = 149,781,812 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,402 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4818 >>>>>>> ACTG content number of A's = 37,668,444 bp (25.15%) number of C's = 28,710,363 bp (19.17%) number of T's = 47,329,795 bp (31.6%) number of G's = 36,069,820 bp (24.08%) number of N's = 3,390 bp (0%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 768,642 number of insertions = 9,747 mapped reads with insertion percentage = 0.37% number of deletions = 29,784 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.04% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.4206X There is a 4.19% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% 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 16387827 0.06574838985055126 0.7973247817273811 chr2 243199373 12776581 0.052535419159982784 0.6196346165376223 chr3 198022430 12074171 0.06097375433681932 0.28578162209749114 chr4 191154276 8609448 0.04503926451532792 0.2613842477211875 chr5 180915260 6941029 0.03836618867861119 0.22355649778324269 chr6 171115067 7957646 0.04650464824351207 0.30059596060626065 chr7 159138663 8992440 0.056506947026443224 0.6294857975087418 chr8 146364022 7396674 0.050536148835811576 0.3583834438187859 chr9 141213431 5040338 0.035693049622170854 0.28260823570318117 chr10 135534747 8257015 0.060921757577044065 0.4503013892310104 chr11 135006516 6995946 0.05181932107632494 0.3352185561585967 chr12 133851895 7019789 0.05244444988993245 0.26549079298372585 chr13 115169878 4886772 0.04243099050604186 0.23914870243260455 chr14 107349540 4435372 0.041317102988983466 0.2421025338589547 chr15 102531392 4309054 0.04202667998499426 0.24387164744257234 chr16 90354753 4169861 0.04614987990725845 0.27746450782095183 chr17 81195210 3170304 0.0390454560065797 0.238423823412705 chr18 78077248 3304611 0.042324890856808885 0.5648606697190034 chr19 59128983 2816610 0.04763501513293405 0.5443818402947225 chr20 63025520 2871254 0.0455570061143486 0.24951963448022818 chr21 48129895 1986974 0.04128357229950325 0.24833437623193036 chr22 51304566 1267775 0.02471076356049869 0.17719303575197048 chrMT 16571 11637 0.7022509202824211 0.962181210868655 chrX 155270560 7730574 0.049787764016565664 0.2884955139807112 chrY 59373566 419214 0.007060616840834522 0.18201814042329695