BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068137.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 = 1,949,609 number of mapped reads = 1,629,258 (83.57%) number of supplementary alignments = 13,136 (0.67%) number of secondary alignments = 0 number of mapped bases = 106,542,744 bp number of sequenced bases = 106,487,052 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 206,277 duplication rate = 9.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2281 >>>>>>> ACTG content number of A's = 29,082,194 bp (27.31%) number of C's = 18,819,992 bp (17.67%) number of T's = 34,727,825 bp (32.61%) number of G's = 23,755,802 bp (22.31%) number of N's = 101,239 bp (0.1%) GC percentage = 39.98% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 936,936 number of insertions = 7,620 mapped reads with insertion percentage = 0.46% number of deletions = 33,948 mapped reads with deletion percentage = 2.06% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.0344X std coverageData = 0.4166X There is a 1.96% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 6882068 0.027611036523756544 0.8443749502712673 chr2 243199373 15057560 0.06191446883376628 0.4816066210099929 chr3 198022430 10331597 0.052173872424452115 0.36849983599219105 chr4 191154276 9556301 0.04999260911118724 0.3643548904918205 chr5 180915260 2015670 0.011141514541117207 0.17052090923078406 chr6 171115067 4173046 0.024387367361402488 0.2659331191308032 chr7 159138663 5204224 0.03270244893285298 0.3407730628120221 chr8 146364022 1425769 0.009741253215903018 0.20790970845122636 chr9 141213431 1705582 0.012078043766247703 0.19998485088511966 chr10 135534747 3968310 0.02927891251385152 0.4489087635852872 chr11 135006516 12578608 0.09317037705054176 0.6089139239057032 chr12 133851895 5419105 0.04048582950581312 0.3296750924531527 chr13 115169878 977094 0.008483937093343105 0.14987786717485402 chr14 107349540 955469 0.00890054116673439 0.1552623183416386 chr15 102531392 851216 0.008302003741449253 0.1423789005105789 chr16 90354753 1866066 0.02065266007644335 0.23372086358923402 chr17 81195210 4183247 0.05152085942015545 0.40721423251375216 chr18 78077248 6082371 0.0779019644749774 0.5605371817965252 chr19 59128983 2927790 0.04951531129835262 0.5446516417667655 chr20 63025520 594484 0.009432433084249047 0.16510855172656916 chr21 48129895 3305433 0.06867733661168386 0.4254572200988461 chr22 51304566 618969 0.012064598694782838 0.1691869108295459 chrMT 16571 7340 0.44294248989198 1.0088482735846596 chrX 155270560 5735030 0.03693572046110995 0.4375040242034897 chrY 59373566 120395 0.0020277542366244263 0.06588697670216666