BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173982.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,231,920 number of mapped reads = 3,156,585 (97.67%) number of supplementary alignments = 399,827 (12.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,579,785 number of mapped paired reads (second in pair) = 1,576,800 number of mapped paired reads (both in pair) = 3,109,180 number of mapped paired reads (singletons) = 47,405 number of mapped bases = 356,137,095 bp number of sequenced bases = 355,896,309 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,500,392 duplication rate = 64.45% >>>>>>> Insert size mean insert size = 1,078,329.7734 std insert size = 9,772,994.1356 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 52.5512 >>>>>>> ACTG content number of A's = 106,172,190 bp (29.83%) number of C's = 70,837,447 bp (19.9%) number of T's = 105,273,199 bp (29.58%) number of G's = 73,610,898 bp (20.68%) number of N's = 2,575 bp (0%) GC percentage = 40.59% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,086,449 number of insertions = 39,954 mapped reads with insertion percentage = 1.22% number of deletions = 100,495 mapped reads with deletion percentage = 3.1% homopolymer indels = 40.89% >>>>>>> Coverage mean coverageData = 0.115X std coverageData = 2.0802X There is a 2.54% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 1.41% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.84% of reference with a coverageData >= 5X There is a 0.69% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 28203641 0.11315374415857524 1.2954758389458152 chr2 243199373 29904292 0.12296204398520386 6.221492306922001 chr3 198022430 22621493 0.11423702355334191 0.9983893690163486 chr4 191154276 24948648 0.13051577250618238 1.3755939623329296 chr5 180915260 21548350 0.11910742078915841 1.0185979861867045 chr6 171115067 21494337 0.12561335116094716 1.1595799037449577 chr7 159138663 21217260 0.13332561427891348 1.4178284274609358 chr8 146364022 16077308 0.1098446720738516 1.4569458633678327 chr9 141213431 15436222 0.10931128781935763 1.2229953914956704 chr10 135534747 18794510 0.13866931112506523 1.5178393583530438 chr11 135006516 16677161 0.12352856361392216 1.0667758089898196 chr12 133851895 16945616 0.1265997466827048 1.0706802086285179 chr13 115169878 12844585 0.11152729535755869 1.0057098877244646 chr14 107349540 10956726 0.10206588682168549 0.9383516819472913 chr15 102531392 10379236 0.1012298360291451 0.9476418392984436 chr16 90354753 10714385 0.11858131027152495 1.122799858723345 chr17 81195210 10182898 0.12541254588786704 1.075579200853747 chr18 78077248 10316114 0.1321270186162299 1.5800467569543188 chr19 59128983 6913500 0.1169223559958743 1.1052739692686986 chr20 63025520 7891292 0.12520788404443153 1.0841507464365425 chr21 48129895 4938074 0.10259889409690173 1.113121879852663 chr22 51304566 4701088 0.09163098660653322 1.0224194836329197 chrMT 16571 530623 32.0211815822823 25.98022396790509 chrX 155270560 8951115 0.057648500784694794 0.6960414379502965 chrY 59373566 2948621 0.04966218468333197 0.9700929106092061