BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237259.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 = 3,839,941 number of mapped reads = 3,537,060 (92.11%) number of supplementary alignments = 43,157 (1.12%) number of secondary alignments = 0 number of mapped bases = 225,564,119 bp number of sequenced bases = 225,444,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,187,181 duplication rate = 19.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7579 >>>>>>> ACTG content number of A's = 60,940,817 bp (27.03%) number of C's = 39,486,097 bp (17.51%) number of T's = 74,392,555 bp (33%) number of G's = 50,599,349 bp (22.44%) number of N's = 25,656 bp (0.01%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,499,506 number of insertions = 23,556 mapped reads with insertion percentage = 0.66% number of deletions = 65,386 mapped reads with deletion percentage = 1.82% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.0729X std coverageData = 1.2676X There is a 2.07% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 15711791 0.0630361157655852 0.766967425806852 chr2 243199373 11491661 0.047252017380817836 1.3265944834174956 chr3 198022430 21217883 0.10714888712354453 0.817979912153137 chr4 191154276 10284697 0.05380312287651886 1.211499583089608 chr5 180915260 9972894 0.05512466996979691 0.5736165123120612 chr6 171115067 29919543 0.1748504297403571 1.2943362758030665 chr7 159138663 12169798 0.07647291846356657 0.9585809263578636 chr8 146364022 21101441 0.14417095616571673 3.821644336960065 chr9 141213431 7683673 0.054411771922742956 0.8186733317478191 chr10 135534747 6360616 0.04692978103983918 1.6366153135172088 chr11 135006516 7683464 0.05691180120520998 0.6525522260405852 chr12 133851895 3640875 0.027200772913973315 0.4461914230395276 chr13 115169878 7925625 0.06881682205133534 0.6552555314534143 chr14 107349540 13488616 0.12565136282838288 0.9142739018504082 chr15 102531392 5722391 0.05581111197632038 0.574802912486059 chr16 90354753 3298513 0.03650624776761882 0.6166997597284404 chr17 81195210 3760356 0.04631253493894529 0.6305438373119177 chr18 78077248 10835346 0.13877725300973723 2.0298230995861473 chr19 59128983 1895673 0.03205996287810328 0.5336936288874422 chr20 63025520 2652068 0.04207927201552641 0.584502073612471 chr21 48129895 4851649 0.1008032325854856 1.0837817113503456 chr22 51304566 2124471 0.04140900441492868 0.48076651728708625 chrMT 16571 36421 2.197875807132943 3.4922584645475023 chrX 155270560 10380611 0.06685498525927903 0.6606706018498372 chrY 59373566 1354043 0.022805485525326203 1.1159617770408703