BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234142.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 = 1,136,084 number of mapped reads = 849,383 (74.76%) number of supplementary alignments = 5,948 (0.52%) number of secondary alignments = 0 number of mapped bases = 55,767,510 bp number of sequenced bases = 55,738,036 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,625 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.693 >>>>>>> ACTG content number of A's = 15,679,680 bp (28.13%) number of C's = 9,623,455 bp (17.27%) number of T's = 18,362,074 bp (32.94%) number of G's = 12,064,174 bp (21.64%) number of N's = 8,653 bp (0.02%) GC percentage = 38.91% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 483,295 number of insertions = 4,862 mapped reads with insertion percentage = 0.57% number of deletions = 16,730 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.018X std coverageData = 0.2374X There is a 1.5% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4330438 0.017373830334408674 0.28500969823717826 chr2 243199373 4724452 0.01942625074119743 0.2272064091290608 chr3 198022430 3575742 0.01805725745310771 0.1557777451607433 chr4 191154276 3563976 0.018644500528986335 0.16960303571288857 chr5 180915260 3707398 0.020492455970823026 0.1667414400421331 chr6 171115067 3231491 0.018884900416162653 0.1684057485027915 chr7 159138663 3012017 0.018926997017688907 0.21098351765515883 chr8 146364022 3006045 0.02053814153863577 0.6791859331533023 chr9 141213431 2350117 0.01664230507932351 0.17801760787842388 chr10 135534747 2454209 0.018107600112316585 0.18792082282817876 chr11 135006516 2544012 0.01884362381442389 0.1900993657432676 chr12 133851895 2579844 0.01927386982455497 0.16378904522778742 chr13 115169878 1846491 0.016032759885358218 0.14767014984551297 chr14 107349540 1834843 0.01709222973847862 0.15542705842942467 chr15 102531392 1405467 0.013707675011376028 0.1355975559933816 chr16 90354753 1419665 0.015712123080011076 0.15348151133189838 chr17 81195210 1328533 0.01636220905149454 0.15349758451797724 chr18 78077248 1501727 0.019233861828736588 0.28707241810445105 chr19 59128983 1019617 0.017243946171034263 0.2016629346285086 chr20 63025520 1209814 0.019195621075399297 0.16231034810807207 chr21 48129895 838663 0.017424991265823454 0.1584950801783609 chr22 51304566 542410 0.010572353345704163 0.11673276668754207 chrMT 16571 39864 2.405648421941947 2.2239078137705612 chrX 155270560 3533649 0.022758010275740616 0.182814783909036 chrY 59373566 167026 0.0028131374153945884 0.07654577690702694