BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231821.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 = 1,477,018 number of mapped reads = 710,888 (48.13%) number of supplementary alignments = 3,235 (0.22%) number of secondary alignments = 0 number of mapped bases = 46,163,049 bp number of sequenced bases = 46,137,734 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,189 duplication rate = 11.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8026 >>>>>>> ACTG content number of A's = 12,834,068 bp (27.82%) number of C's = 8,148,145 bp (17.66%) number of T's = 15,070,939 bp (32.67%) number of G's = 10,069,193 bp (21.82%) number of N's = 15,389 bp (0.03%) GC percentage = 39.48% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 419,079 number of insertions = 4,138 mapped reads with insertion percentage = 0.57% number of deletions = 14,558 mapped reads with deletion percentage = 2.02% homopolymer indels = 48.14% >>>>>>> Coverage mean coverageData = 0.0149X std coverageData = 0.2473X There is a 0.73% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 3934389 0.015784871404593212 0.257617881813947 chr2 243199373 4125273 0.016962514948589115 0.26548736593092626 chr3 198022430 3313999 0.016735472845172135 0.2727613260216803 chr4 191154276 3216364 0.016826011258047925 0.2519036257576518 chr5 180915260 2857753 0.015796085968646314 0.2740234617396044 chr6 171115067 2838100 0.016585915254324155 0.25156593139470523 chr7 159138663 2567011 0.01613065581680801 0.27854634834024106 chr8 146364022 2362481 0.0161411320057876 0.3142906700022957 chr9 141213431 1891155 0.01339217513948797 0.227467203034432 chr10 135534747 2209605 0.01630286733777575 0.2494214254072708 chr11 135006516 2056261 0.015230827821673436 0.2386901539292404 chr12 133851895 2177733 0.016269721097336723 0.23744562874727584 chr13 115169878 1394360 0.0121069851267881 0.2066413469554624 chr14 107349540 1427337 0.0132961631693997 0.2163954614147001 chr15 102531392 1379451 0.013453938087566392 0.21832399006192568 chr16 90354753 1278591 0.01415078850362194 0.22474629439526078 chr17 81195210 1237067 0.015235714027958053 0.22412012495593264 chr18 78077248 1245727 0.015955057739740007 0.3208852547102263 chr19 59128983 800898 0.013544931087348484 0.21290634154559462 chr20 63025520 993682 0.015766343538300042 0.22305485711660195 chr21 48129895 629510 0.013079396911212874 0.2166227518901348 chr22 51304566 473400 0.009227248896326304 0.16525718780596724 chrMT 16571 6579 0.3970188884195281 0.9252104009288048 chrX 155270560 1483067 0.009551501585361707 0.17683112888833402 chrY 59373566 263256 0.0044338923486589975 0.11321688928760391