BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240239.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 = 2,934,812 number of mapped reads = 2,187,842 (74.55%) number of supplementary alignments = 16,837 (0.57%) number of secondary alignments = 0 number of mapped bases = 142,547,490 bp number of sequenced bases = 142,475,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 344,436 duplication rate = 11.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7558 >>>>>>> ACTG content number of A's = 39,992,516 bp (28.07%) number of C's = 25,594,836 bp (17.96%) number of T's = 46,301,786 bp (32.5%) number of G's = 30,533,040 bp (21.43%) number of N's = 53,414 bp (0.04%) GC percentage = 39.39% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,291,136 number of insertions = 10,887 mapped reads with insertion percentage = 0.49% number of deletions = 41,420 mapped reads with deletion percentage = 1.87% homopolymer indels = 48.44% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.5103X There is a 2.08% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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% 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 11203098 0.04494712171649915 0.7407943365472902 chr2 243199373 14824909 0.060957842189831635 0.5740931203950455 chr3 198022430 9209072 0.04650519640628589 0.40911602625913296 chr4 191154276 9628588 0.05037076962902991 0.43552273926253804 chr5 180915260 7554448 0.041756831347449626 0.3850409020028361 chr6 171115067 7699419 0.04499556430060014 0.4542694443092639 chr7 159138663 8546016 0.05370169535733752 0.6880453840505611 chr8 146364022 8015983 0.054767441413983556 0.7447875436668909 chr9 141213431 5290058 0.03746143665328831 0.43172453129550703 chr10 135534747 6495914 0.04792803427743883 0.47615662124698827 chr11 135006516 6266061 0.04641302646458931 0.510221014379489 chr12 133851895 7186395 0.05368915397126055 0.4461899812417376 chr13 115169878 3812496 0.033103239025745954 0.34680761127523574 chr14 107349540 4619275 0.043030226305580815 0.40227959470582175 chr15 102531392 4082817 0.03982016551574761 0.38352523346991285 chr16 90354753 4242894 0.04695817164150734 0.42255563350291636 chr17 81195210 3383118 0.0416664726897067 0.3981468150527697 chr18 78077248 3324171 0.042575411981733785 0.6773736198077734 chr19 59128983 2398079 0.040556743551635244 0.5204756596389839 chr20 63025520 2915101 0.04625270842668176 0.4047028310252006 chr21 48129895 2363880 0.049114588760270514 0.430318536711526 chr22 51304566 1336441 0.02604916295364432 0.2980756395362173 chrMT 16571 36543 2.2052380665017197 2.8393290287920303 chrX 155270560 7727870 0.04977034925358677 0.4360114564096202 chrY 59373566 384844 0.006481739702142869 0.14481425878870627