BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038446.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 16,037,618 number of mapped reads = 15,369,506 (95.83%) number of supplementary alignments = 264,696 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,804,748 number of mapped paired reads (second in pair) = 7,564,758 number of mapped paired reads (both in pair) = 15,071,536 number of mapped paired reads (singletons) = 297,970 number of mapped bases = 2,069,389,116 bp number of sequenced bases = 2,067,870,061 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,085,637 duplication rate = 13.29% >>>>>>> Insert size mean insert size = 105,147.7456 std insert size = 3,124,567.4848 median insert size = 269 >>>>>>> Mapping quality mean mapping quality = 53.4113 >>>>>>> ACTG content number of A's = 591,899,655 bp (28.62%) number of C's = 409,539,239 bp (19.8%) number of T's = 604,761,342 bp (29.25%) number of G's = 461,511,346 bp (22.32%) number of N's = 158,479 bp (0.01%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0144 number of mismatches = 28,684,692 number of insertions = 378,464 mapped reads with insertion percentage = 2.32% number of deletions = 757,281 mapped reads with deletion percentage = 4.73% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.6685X std coverageData = 10.1267X There is a 27.33% of reference with a coverageData >= 1X There is a 14.8% of reference with a coverageData >= 2X There is a 8.02% of reference with a coverageData >= 3X There is a 4.69% of reference with a coverageData >= 4X There is a 2.75% of reference with a coverageData >= 5X There is a 1.67% of reference with a coverageData >= 6X There is a 1.03% of reference with a coverageData >= 7X There is a 0.65% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.02% 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 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 162743240 0.652930128507082 15.882042494462047 chr2 243199373 184046270 0.7567711533532613 9.344526494474103 chr3 198022430 136757342 0.690615411597565 1.5876197587775072 chr4 191154276 138115084 0.7225320138797209 8.5654231717821 chr5 180915260 123553201 0.6829341040661799 1.5181779409904474 chr6 171115067 118222961 0.6908974357003875 6.666631484146602 chr7 159138663 108494976 0.6817637772915058 9.29406370885489 chr8 146364022 104297967 0.7125929280626082 3.079085526037466 chr9 141213431 85287978 0.603965057686333 15.025330120138316 chr10 135534747 118167496 0.8718612652148898 27.16063394939856 chr11 135006516 94636551 0.7009776550340726 6.736380325601637 chr12 133851895 88419555 0.6605775360894218 1.588919728179469 chr13 115169878 62109409 0.5392851853155562 1.304746242872124 chr14 107349540 58922737 0.5488867208932614 1.4942943498994696 chr15 102531392 55060395 0.5370101188131728 1.3185733397413668 chr16 90354753 74523955 0.8247928584343538 16.050922477907537 chr17 81195210 51939685 0.6396890284537721 11.40169718820218 chr18 78077248 58105954 0.7442110920712779 11.309883510334947 chr19 59128983 28400504 0.48031443395534135 7.172981787872528 chr20 63025520 41974544 0.6659928232246239 2.6793797527386585 chr21 48129895 26092368 0.542123933576003 4.058488708955026 chr22 51304566 19606268 0.3821544460584658 1.2045892089930854 chrMT 16571 1082284 65.31193048096071 35.5289294612727 chrX 155270560 120474716 0.7759018580212501 3.529203528597271 chrY 59373566 8353676 0.14069688857832793 10.450208589942504