BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063597.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 = 1,710,194 number of mapped reads = 893,703 (52.26%) number of supplementary alignments = 8,439 (0.49%) number of secondary alignments = 0 number of mapped bases = 57,373,178 bp number of sequenced bases = 57,350,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,366 duplication rate = 12.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6415 >>>>>>> ACTG content number of A's = 16,025,602 bp (27.94%) number of C's = 10,660,311 bp (18.59%) number of T's = 18,096,429 bp (31.55%) number of G's = 12,566,831 bp (21.91%) number of N's = 1,338 bp (0%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 464,574 number of insertions = 4,619 mapped reads with insertion percentage = 0.51% number of deletions = 13,977 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.3669X There is a 0.69% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 5101096 0.020465730354188364 0.41452881266053704 chr2 243199373 4683376 0.019257352279440292 0.4175390901834878 chr3 198022430 3479383 0.017570650961105768 0.296973818413194 chr4 191154276 3805034 0.019905565701287268 0.5095176619397501 chr5 180915260 3329240 0.01840220664636029 0.3227625254691932 chr6 171115067 3505353 0.020485355623301133 0.36618443550111357 chr7 159138663 3068340 0.01928092106693142 0.3362026054247603 chr8 146364022 3081591 0.021054292973720003 0.38076676921525593 chr9 141213431 2350251 0.016643253997560614 0.29781478235334746 chr10 135534747 3001824 0.022148003124246803 0.35134030252569687 chr11 135006516 2848800 0.021101203737455162 0.3529214368499764 chr12 133851895 2560660 0.01913054723655575 0.32399088367751067 chr13 115169878 1859393 0.016144785705165025 0.3208692762982582 chr14 107349540 1664538 0.01550577673644433 0.37526592102365364 chr15 102531392 1661790 0.01620762156433027 0.5481131505819876 chr16 90354753 1525570 0.016884225227199724 0.29086344998116576 chr17 81195210 1217911 0.014999788780643588 0.26361234544735124 chr18 78077248 1470523 0.01883420634907624 0.3621641598065745 chr19 59128983 1013969 0.017148426178748923 0.31014612951598486 chr20 63025520 1128922 0.017912140986698723 0.3207565628355623 chr21 48129895 836748 0.0173852031050556 0.2985652881109396 chr22 51304566 653393 0.01273557211262639 0.24789669353372365 chrMT 16571 11051 0.6668879367569851 1.8213829043091496 chrX 155270560 3325396 0.021416783709674262 0.3581761074409994 chrY 59373566 189026 0.0031836726801957624 0.19867724528205716