BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230370.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,538,402 number of mapped reads = 4,241,262 (93.45%) number of supplementary alignments = 35,534 (0.78%) number of secondary alignments = 0 number of mapped bases = 303,718,324 bp number of sequenced bases = 303,572,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,812 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9818 >>>>>>> ACTG content number of A's = 89,896,087 bp (29.61%) number of C's = 61,954,984 bp (20.41%) number of T's = 88,282,363 bp (29.08%) number of G's = 63,274,145 bp (20.84%) number of N's = 164,427 bp (0.05%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 2,707,718 number of insertions = 27,175 mapped reads with insertion percentage = 0.64% number of deletions = 86,193 mapped reads with deletion percentage = 2.01% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.0981X std coverageData = 1.0025X There is a 5.49% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 23178537 0.09299289569272527 2.194584337220981 chr2 243199373 25790350 0.10604612043962794 0.9591295575944548 chr3 198022430 18391333 0.09287499905944999 0.4755376266985505 chr4 191154276 17702511 0.09260850120873049 0.6021970590211149 chr5 180915260 19915886 0.11008405813860037 0.5255352667586088 chr6 171115067 17895951 0.10458430875639957 0.6180234297547097 chr7 159138663 15944465 0.1001922769704305 1.1812189031282538 chr8 146364022 15851122 0.10829930595921995 1.1936751572382631 chr9 141213431 12247786 0.08673244402651756 0.8624196581022617 chr10 135534747 15208493 0.11221102585597478 0.9626188543177159 chr11 135006516 14977418 0.11093848240628623 0.8999398174418144 chr12 133851895 14145349 0.10567910898833371 0.529052353625978 chr13 115169878 8734715 0.07584200966158877 0.42617653281108253 chr14 107349540 9192839 0.08563463802453182 0.5240026180277848 chr15 102531392 9630871 0.09393094945984932 0.4773472733863959 chr16 90354753 8633986 0.09555652263251718 0.607026864325903 chr17 81195210 8291884 0.1021228222699344 0.6243958511926715 chr18 78077248 8211031 0.1051654766315534 1.885766988603316 chr19 59128983 6117349 0.10345770702668775 1.312926166926336 chr20 63025520 6630651 0.10520581186795444 0.5614200741546505 chr21 48129895 4292953 0.08919514576127789 0.5944014750633113 chr22 51304566 3538916 0.06897857785211554 0.4042984309475166 chrMT 16571 280660 16.93681733148271 12.759388193072477 chrX 155270560 17923521 0.1154341235067356 0.6416569255104164 chrY 59373566 989747 0.016669825760507632 0.48622172941546776