BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173932.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 = 3,810,592 number of mapped reads = 3,724,565 (97.74%) number of supplementary alignments = 472,294 (12.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,864,863 number of mapped paired reads (second in pair) = 1,859,702 number of mapped paired reads (both in pair) = 3,671,486 number of mapped paired reads (singletons) = 53,079 number of mapped bases = 422,403,126 bp number of sequenced bases = 422,111,978 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,926,926 duplication rate = 63.82% >>>>>>> Insert size mean insert size = 1,322,463.2802 std insert size = 10,692,641.4613 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 52.6307 >>>>>>> ACTG content number of A's = 126,487,433 bp (29.97%) number of C's = 83,508,744 bp (19.78%) number of T's = 125,293,382 bp (29.68%) number of G's = 86,818,960 bp (20.57%) number of N's = 3,459 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,669,370 number of insertions = 45,664 mapped reads with insertion percentage = 1.18% number of deletions = 123,618 mapped reads with deletion percentage = 3.24% homopolymer indels = 40.71% >>>>>>> Coverage mean coverageData = 0.1364X std coverageData = 2.6539X There is a 3.05% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 1.32% of reference with a coverageData >= 4X There is a 0.98% of reference with a coverageData >= 5X There is a 0.81% of reference with a coverageData >= 6X There is a 0.6% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.01% 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 0.01% 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 33707965 0.13523723577804045 1.2938360324132017 chr2 243199373 39607704 0.16286104487613132 8.463089633079266 chr3 198022430 28610409 0.1444806479750804 1.125630185463555 chr4 191154276 29979475 0.15683392298271162 1.4143143262214437 chr5 180915260 27883263 0.15412333376410592 1.1773185839544833 chr6 171115067 23938288 0.13989585148571398 1.2225449047060568 chr7 159138663 21922064 0.13775448144867222 1.2793073078045745 chr8 146364022 21835969 0.1491894572287717 1.5958312015198506 chr9 141213431 18428577 0.13050158805361792 1.3265602681412088 chr10 135534747 18923137 0.13961834451205343 1.552401702624266 chr11 135006516 19483301 0.14431378260290784 1.1317837060746183 chr12 133851895 17712607 0.13232989342437027 1.1033054240323772 chr13 115169878 14746461 0.12804095355558162 1.0650124204555547 chr14 107349540 13885387 0.12934742896895507 1.07392410607125 chr15 102531392 12324221 0.12019948973286153 1.0387591480078502 chr16 90354753 12139459 0.13435329738547347 1.1999365108611952 chr17 81195210 11833273 0.1457385601933907 1.1854739612396394 chr18 78077248 11913497 0.15258602608534563 1.6363226379827278 chr19 59128983 7764166 0.13130897245433767 1.1284521656145763 chr20 63025520 9352969 0.14839971173581748 1.1651047814234952 chr21 48129895 5959424 0.12381959279154879 1.2174455818052392 chr22 51304566 5282363 0.1029608748663813 1.0103460321341033 chrMT 16571 444784 26.841107959688614 25.718157377756018 chrX 155270560 11272521 0.07259921649023485 0.7919615931910702 chrY 59373566 3451842 0.05813769043280978 0.990386592228889