BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716173.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 = 2,250,550 number of mapped reads = 1,960,466 (87.11%) number of supplementary alignments = 59,126 (2.63%) number of secondary alignments = 0 number of mapped bases = 146,953,203 bp number of sequenced bases = 146,901,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,919 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8088 >>>>>>> ACTG content number of A's = 37,214,750 bp (25.33%) number of C's = 29,957,595 bp (20.39%) number of T's = 44,046,140 bp (29.98%) number of G's = 35,666,004 bp (24.28%) number of N's = 16,911 bp (0.01%) GC percentage = 44.67% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,066,273 number of insertions = 12,026 mapped reads with insertion percentage = 0.61% number of deletions = 29,703 mapped reads with deletion percentage = 1.49% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0475X std coverageData = 0.3457X There is a 4.11% 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 14697910 0.058968398718653545 0.5017412804115674 chr2 243199373 14297470 0.05878909071036133 0.48302388665056706 chr3 198022430 9867998 0.04983272854494312 0.251611101175019 chr4 191154276 5790096 0.0302901725305899 0.2083826626400049 chr5 180915260 8088385 0.04470814125906239 0.23595192427216136 chr6 171115067 9031063 0.052777719451204144 0.30714854571465144 chr7 159138663 8534474 0.053629167413578184 0.47325096718872617 chr8 146364022 9251403 0.06320817693845554 0.4034722994539039 chr9 141213431 7394974 0.052367355906818805 0.3355222581158681 chr10 135534747 7876564 0.05811472094310989 0.40650966893342 chr11 135006516 6353170 0.047058247173788266 0.30568288055047954 chr12 133851895 5764512 0.0430663458294707 0.232623370742251 chr13 115169878 4596780 0.039913040456637454 0.2234477159670137 chr14 107349540 3762756 0.03505144036946968 0.22970740279779656 chr15 102531392 4108856 0.040074126761099664 0.22492013687367077 chr16 90354753 3931127 0.0435076946090484 0.256726015379656 chr17 81195210 4984438 0.0613883257399051 0.32360648701012484 chr18 78077248 2021645 0.02589288239257613 0.5291215576721927 chr19 59128983 2968504 0.05020387379231603 0.42523145269405077 chr20 63025520 2676287 0.042463544925928416 0.2429313321960686 chr21 48129895 2477977 0.051485194389059026 0.26561392615992546 chr22 51304566 1711450 0.03335862932745596 0.20681572520656297 chrMT 16571 23466 1.4160883471124253 1.8674909614511714 chrX 155270560 6410573 0.04128646795632089 0.2662547900655645 chrY 59373566 331325 0.005580345300465867 0.15652205726226304