BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240073.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 = 2,301,432 number of mapped reads = 1,835,352 (79.75%) number of supplementary alignments = 16,207 (0.7%) number of secondary alignments = 0 number of mapped bases = 120,617,441 bp number of sequenced bases = 120,557,491 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 282,403 duplication rate = 11.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6778 >>>>>>> ACTG content number of A's = 34,344,611 bp (28.49%) number of C's = 22,566,804 bp (18.72%) number of T's = 38,181,729 bp (31.67%) number of G's = 25,453,232 bp (21.11%) number of N's = 11,115 bp (0.01%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,025,180 number of insertions = 8,724 mapped reads with insertion percentage = 0.47% number of deletions = 34,316 mapped reads with deletion percentage = 1.85% homopolymer indels = 48.34% >>>>>>> Coverage mean coverageData = 0.039X std coverageData = 0.4593X There is a 1.67% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 9596237 0.03850035342539829 0.6528163610510865 chr2 243199373 12890538 0.05300399355881563 0.5267932967004797 chr3 198022430 7554658 0.03815051658541914 0.3771450955097539 chr4 191154276 8061361 0.04217201502727567 0.4060724521590686 chr5 180915260 6335616 0.03501979877208811 0.36884060516901107 chr6 171115067 6141522 0.03589118192613629 0.4024894782951936 chr7 159138663 7142440 0.04488186506882994 0.5815497910247798 chr8 146364022 7006360 0.04786941424717066 0.5931705365354769 chr9 141213431 4475182 0.03169090906090937 0.4141075759611978 chr10 135534747 5585604 0.04121160162714584 0.44667608725612484 chr11 135006516 5317408 0.03938630636168702 0.4674546675263805 chr12 133851895 5853245 0.043729265095574475 0.4075534240215976 chr13 115169878 3117606 0.027069630133670888 0.32113566866519616 chr14 107349540 3983825 0.0371107784905273 0.3911497989643599 chr15 102531392 3505560 0.03419011418473671 0.3730629269953004 chr16 90354753 3663026 0.04054049043773049 0.38989840377962975 chr17 81195210 2773162 0.034154256143927704 0.364215546038826 chr18 78077248 2932591 0.03756012250841628 0.6185275327023461 chr19 59128983 2105422 0.03560727570775232 0.4688819061423934 chr20 63025520 2451171 0.03889172195643923 0.3794505355655169 chr21 48129895 2033928 0.04225914060273765 0.40839287946460895 chr22 51304566 1088248 0.021211523356420167 0.2660800854649317 chrMT 16571 20146 1.2157383380604672 2.160540070394719 chrX 155270560 6663865 0.042917762388439896 0.41673298451173363 chrY 59373566 318720 0.0053680454362468304 0.130681763339037