BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714213.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 156,724 number of mapped reads = 25,985 (16.58%) number of supplementary alignments = 400 (0.26%) number of secondary alignments = 0 number of mapped bases = 2,651,652 bp number of sequenced bases = 2,646,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,276 duplication rate = 40.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 6.8517 >>>>>>> ACTG content number of A's = 65,333 bp (2.47%) number of C's = 29,797 bp (1.13%) number of T's = 39,416 bp (1.49%) number of G's = 2,511,510 bp (94.91%) number of N's = 53 bp (0%) GC percentage = 96.04% >>>>>>> Mismatches and indels general error rate = 0.0315 number of mismatches = 64,997 number of insertions = 2,745 mapped reads with insertion percentage = 7.27% number of deletions = 1,229 mapped reads with deletion percentage = 4.56% homopolymer indels = 61.1% >>>>>>> Coverage mean coverageData = 0.0009X std coverageData = 3.2438X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 21165 8.491453267031178E-5 0.21135912538580012 chr2 243199373 2514961 0.010341149193670001 11.56906407137632 chr3 198022430 1801 9.09492929664584E-6 0.0039877507740199635 chr4 191154276 1272 6.654310992237495E-6 0.004216179940678041 chr5 180915260 1617 8.937886168364129E-6 0.0034368709469810997 chr6 171115067 1253 7.3225579837455225E-6 0.0038200086598070134 chr7 159138663 5688 3.574241414859694E-5 0.029384682058287846 chr8 146364022 10738 7.336502409041479E-5 0.06560688064439536 chr9 141213431 1297 9.184678757645935E-6 0.004614534095872523 chr10 135534747 19524 1.4405162094706237E-4 0.27431693749542463 chr11 135006516 1585 1.1740174081671732E-5 0.00915198243777347 chr12 133851895 3289 2.4571934525095816E-5 0.02277268031160902 chr13 115169878 812 7.050454633632589E-6 0.0041962746839743405 chr14 107349540 3349 3.1197152777738966E-5 0.039040613565618575 chr15 102531392 946 9.226442570876244E-6 0.0048481863902133365 chr16 90354753 830 9.186013711973736E-6 0.0041922647841354 chr17 81195210 3370 4.1504911435046476E-5 0.03778939246206549 chr18 78077248 815 1.0438380205203954E-5 0.0049885370363027095 chr19 59128983 955 1.6151131840031817E-5 0.007432019870947404 chr20 63025520 965 1.5311258042773784E-5 0.007230503105029627 chr21 48129895 674 1.4003770421689057E-5 0.005079859382702528 chr22 51304566 260 5.067775059241316E-6 0.0025207507977273633 chrMT 16571 294 0.017741838150986664 0.13201161058789812 chrX 155270560 53874 3.469685431674878E-4 0.07447327873508283 chrY 59373566 318 5.35591882758061E-6 0.002837374150079761