BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237296.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 = 5,581,504 number of mapped reads = 5,223,993 (93.59%) number of supplementary alignments = 36,600 (0.66%) number of secondary alignments = 0 number of mapped bases = 370,325,227 bp number of sequenced bases = 370,152,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 390,031 duplication rate = 4.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4062 >>>>>>> ACTG content number of A's = 109,042,770 bp (29.46%) number of C's = 71,779,317 bp (19.39%) number of T's = 113,343,506 bp (30.62%) number of G's = 75,980,273 bp (20.53%) number of N's = 6,371 bp (0%) GC percentage = 39.92% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 2,855,951 number of insertions = 36,533 mapped reads with insertion percentage = 0.69% number of deletions = 94,158 mapped reads with deletion percentage = 1.78% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.1196X std coverageData = 1.4302X There is a 5.56% of reference with a coverageData >= 1X There is a 2.72% of reference with a coverageData >= 2X There is a 1.48% of reference with a coverageData >= 3X There is a 0.82% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 49101729 0.19699741891515687 2.3545272454250776 chr2 243199373 31177751 0.1281983198205038 1.8062891770296998 chr3 198022430 14307260 0.07225070412478021 0.47841666948319683 chr4 191154276 11332998 0.05928718016226851 1.378678901759535 chr5 180915260 26847038 0.1483956521965035 0.7353059803043811 chr6 171115067 41385986 0.24186056041458934 1.1586217639456577 chr7 159138663 23127319 0.14532809666749558 1.484138796095921 chr8 146364022 15045116 0.10279244717667023 2.8448950470406094 chr9 141213431 17236688 0.12206125067522791 1.2434710091306747 chr10 135534747 8526239 0.06290814118685004 2.03143608364458 chr11 135006516 11174376 0.08276916056407232 0.7505412843148109 chr12 133851895 17744278 0.13256650568899306 0.7035253153791767 chr13 115169878 14810008 0.12859272109327058 0.6518964747966811 chr14 107349540 2652450 0.02470853624524148 0.5420812498824282 chr15 102531392 9565850 0.0932967924594255 0.54157530340887 chr16 90354753 5678983 0.0628520671181515 0.7268198466566783 chr17 81195210 7418750 0.09136930614502999 0.6601991718959039 chr18 78077248 8675203 0.11111051198935701 2.106153351081451 chr19 59128983 9555959 0.16161209808056398 1.2978940699994261 chr20 63025520 10425366 0.16541499379933716 0.852384659889113 chr21 48129895 9224541 0.19165927953925518 1.3110726948056173 chr22 51304566 5800275 0.1130557268528497 0.5868888523850175 chrMT 16571 31280 1.887635025043751 2.202158549395347 chrX 155270560 18287777 0.11778006725808164 0.6733270459164173 chrY 59373566 1192007 0.020076392244993337 1.3016594883710253