BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234122.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 = 7,553,614 number of mapped reads = 6,625,394 (87.71%) number of supplementary alignments = 74,524 (0.99%) number of secondary alignments = 0 number of mapped bases = 452,891,920 bp number of sequenced bases = 452,747,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,890,522 duplication rate = 12.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7945 >>>>>>> ACTG content number of A's = 111,187,458 bp (24.56%) number of C's = 78,335,851 bp (17.3%) number of T's = 118,088,767 bp (26.08%) number of G's = 145,036,738 bp (32.03%) number of N's = 99,068 bp (0.02%) GC percentage = 49.34% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 2,638,673 number of insertions = 28,195 mapped reads with insertion percentage = 0.42% number of deletions = 88,444 mapped reads with deletion percentage = 1.32% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.1463X std coverageData = 118.8487X There is a 3.54% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 1.69% of reference with a coverageData >= 3X There is a 1.23% of reference with a coverageData >= 4X There is a 0.9% of reference with a coverageData >= 5X There is a 0.66% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 23754948 0.09530547167623707 1.6617411648517446 chr2 243199373 89146297 0.3665564425612232 424.00557312984466 chr3 198022430 33954861 0.17146977238891575 1.1117877682178532 chr4 191154276 26838671 0.14040319453800762 1.0076173039636749 chr5 180915260 15272168 0.08441614046266743 0.7695546423177813 chr6 171115067 24326385 0.1421638984017696 1.3023329656987848 chr7 159138663 19460435 0.12228602800313837 1.26926190466923 chr8 146364022 29647710 0.20256146008340767 1.6350716631132425 chr9 141213431 12844175 0.09095576043329759 0.9994039918696682 chr10 135534747 25247733 0.18628236344440882 1.3277863791874245 chr11 135006516 13342242 0.09882665218914323 1.2972499108441577 chr12 133851895 16644371 0.12434916218406919 0.9546589091631611 chr13 115169878 9131005 0.0792829267388822 0.7562154035829475 chr14 107349540 21607781 0.2012843371289714 1.347533686038179 chr15 102531392 12601818 0.12290692395944454 0.9679997242707067 chr16 90354753 8617753 0.0953768641257865 0.8673330379456101 chr17 81195210 10716669 0.13198646816727244 1.028096500896609 chr18 78077248 8668563 0.11102546800829866 1.8190860975238314 chr19 59128983 11617798 0.19648229025011305 1.5719510952774534 chr20 63025520 8315330 0.1319359205604333 0.991786367427686 chr21 48129895 8877906 0.18445720689812434 1.2160929340053215 chr22 51304566 3130866 0.061025094725487006 0.6661051791245688 chrMT 16571 208651 12.59133425864462 13.042026674626552 chrX 155270560 16072986 0.1035159916986195 0.9040708630537088 chrY 59373566 2844798 0.04791354455617505 0.5931512639211346