BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173935.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 = 4,402,228 number of mapped reads = 4,304,099 (97.77%) number of supplementary alignments = 492,249 (11.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,155,670 number of mapped paired reads (second in pair) = 2,148,429 number of mapped paired reads (both in pair) = 4,246,056 number of mapped paired reads (singletons) = 58,043 number of mapped bases = 486,817,368 bp number of sequenced bases = 486,487,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,436,980 duplication rate = 66.01% >>>>>>> Insert size mean insert size = 773,328.4352 std insert size = 8,293,003.6988 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.8594 >>>>>>> ACTG content number of A's = 145,833,210 bp (29.98%) number of C's = 96,221,790 bp (19.78%) number of T's = 144,581,387 bp (29.72%) number of G's = 99,847,847 bp (20.52%) number of N's = 3,734 bp (0%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 4,109,147 number of insertions = 51,618 mapped reads with insertion percentage = 1.16% number of deletions = 146,472 mapped reads with deletion percentage = 3.32% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 0.1573X std coverageData = 2.9255X There is a 3.25% of reference with a coverageData >= 1X There is a 2.48% of reference with a coverageData >= 2X There is a 1.87% of reference with a coverageData >= 3X There is a 1.52% of reference with a coverageData >= 4X There is a 1.15% of reference with a coverageData >= 5X There is a 0.96% of reference with a coverageData >= 6X There is a 0.73% of reference with a coverageData >= 7X There is a 0.63% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.43% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 38734150 0.155402421244118 1.4254916585541437 chr2 243199373 44575231 0.18328678421387212 9.29303743841683 chr3 198022430 34072972 0.1720662250230946 1.2818632926505165 chr4 191154276 34093910 0.1783580818249653 1.5245152824952013 chr5 180915260 30550951 0.16886884500511454 1.2550003963710599 chr6 171115067 29224726 0.1707899047837792 1.346235194326721 chr7 159138663 26928990 0.16921714366797214 1.5632703034292574 chr8 146364022 25571121 0.1747090620398502 1.85224198312609 chr9 141213431 21045658 0.14903439319451137 1.3654664704238397 chr10 135534747 23322079 0.17207453819941834 1.8166958840071203 chr11 135006516 21742095 0.16104478246072212 1.2513190875124751 chr12 133851895 22107185 0.16516153917731236 1.2861344300415118 chr13 115169878 15397915 0.13369741522171275 1.1226158423892567 chr14 107349540 15221536 0.14179414276018323 1.1702916775221468 chr15 102531392 13949858 0.13605450709183778 1.1478843288747023 chr16 90354753 14400422 0.1593764746388051 1.3848453475700233 chr17 81195210 13355707 0.1644888534680802 1.3022254893182132 chr18 78077248 13110346 0.1679150627849998 1.6391344248239186 chr19 59128983 9133952 0.15447503976180343 1.2706921612163466 chr20 63025520 10406608 0.16511736832952748 1.2771445744448853 chr21 48129895 6885086 0.143052171628465 1.4138145629967114 chr22 51304566 5768870 0.11244359810002096 1.1942887728186402 chrMT 16571 866269 52.276205419105665 48.70118396980233 chrX 155270560 12712336 0.08187215915238535 0.8693127023229062 chrY 59373566 3639395 0.0612965540927759 1.053788695650319