BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867868.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,532,261 number of mapped reads = 1,420,390 (92.7%) number of supplementary alignments = 6,724 (0.44%) number of secondary alignments = 0 number of mapped bases = 84,078,133 bp number of sequenced bases = 84,053,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,483 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7906 >>>>>>> ACTG content number of A's = 22,446,073 bp (26.7%) number of C's = 17,223,334 bp (20.49%) number of T's = 25,465,109 bp (30.3%) number of G's = 18,907,087 bp (22.49%) number of N's = 11,696 bp (0.01%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 419,985 number of insertions = 6,677 mapped reads with insertion percentage = 0.47% number of deletions = 15,651 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.64% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2655X There is a 2.46% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6706725 0.026907555829118676 0.4750819561103231 chr2 243199373 7110446 0.029237106626915522 0.35500131046007066 chr3 198022430 5562118 0.028088323125819634 0.18127827649325726 chr4 191154276 5425587 0.028383288689811992 0.20287346840282408 chr5 180915260 5020865 0.02775257874874679 0.18089442061054506 chr6 171115067 4814887 0.02813829947540505 0.19986490313898791 chr7 159138663 4646728 0.029199239910668345 0.30923685380820115 chr8 146364022 4287912 0.029296215978541502 0.2740930133564073 chr9 141213431 3556122 0.025182604620661048 0.22018535765367633 chr10 135534747 4099327 0.03024557975527855 0.27332698126906246 chr11 135006516 3851053 0.02852494171466509 0.2356395552917777 chr12 133851895 3783976 0.02826987245866037 0.1827074299298374 chr13 115169878 2622320 0.02276914802323573 0.16200219924300902 chr14 107349540 2490406 0.02319903746210743 0.16818185310182604 chr15 102531392 2410016 0.023505152451260974 0.16626549651493694 chr16 90354753 2444365 0.02705297639405865 0.19123662747229395 chr17 81195210 2306797 0.028410505989207985 0.19400417772723277 chr18 78077248 2249175 0.02880704760495657 0.39413484386043346 chr19 59128983 1777922 0.030068536778317327 0.3794566545124213 chr20 63025520 1831825 0.02906481374528921 0.1870105841627932 chr21 48129895 1098914 0.022832254256943633 0.18460396147138422 chr22 51304566 1009843 0.019683296804420877 0.15198790766838968 chrMT 16571 12372 0.7466055156598878 0.971067266532293 chrX 155270560 4681220 0.03014879317753475 0.20294573286091383 chrY 59373566 277212 0.004668946446639234 0.1691937776952318