BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716581.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 = 1,605,261 number of mapped reads = 1,451,122 (90.4%) number of supplementary alignments = 7,280 (0.45%) number of secondary alignments = 0 number of mapped bases = 84,212,702 bp number of sequenced bases = 84,187,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,124 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2423 >>>>>>> ACTG content number of A's = 20,136,813 bp (23.92%) number of C's = 16,724,505 bp (19.87%) number of T's = 27,352,610 bp (32.49%) number of G's = 19,972,344 bp (23.72%) number of N's = 978 bp (0%) GC percentage = 43.59% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 421,814 number of insertions = 5,844 mapped reads with insertion percentage = 0.4% number of deletions = 16,054 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.74% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2652X There is a 2.47% 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 7751956 0.03110104989467609 0.4332266433564529 chr2 243199373 8293496 0.03410163397090666 0.33937385354748983 chr3 198022430 5973453 0.030165537308071616 0.19247240823804923 chr4 191154276 4716285 0.02467266282863586 0.1824038838104945 chr5 180915260 4493809 0.02483930321853447 0.1699794843055144 chr6 171115067 4644389 0.02714190562774931 0.19433283007977395 chr7 159138663 4127268 0.02593504257353224 0.46265601510961657 chr8 146364022 6947315 0.04746600226659527 0.2999262983266488 chr9 141213431 3502708 0.024804354480984177 0.19708633419426674 chr10 135534747 3438001 0.025366196315694603 0.32617946090367134 chr11 135006516 2867755 0.021241604368192123 0.19049220275846218 chr12 133851895 3911183 0.029220228820817217 0.19776164955162176 chr13 115169878 2169664 0.01883881478106628 0.14895070902689111 chr14 107349540 2739162 0.0255162900558307 0.17526378973375142 chr15 102531392 2022736 0.019727967801314937 0.15609470982695592 chr16 90354753 2582613 0.028583034253881475 0.19162144495852673 chr17 81195210 3578630 0.04407439798480723 0.23535526283932176 chr18 78077248 1899817 0.024332530265410993 0.30408002701839565 chr19 59128983 1725365 0.029179683337357588 0.352351759788772 chr20 63025520 1474120 0.0233892556539002 0.17130261333651212 chr21 48129895 864470 0.017961186077800503 0.15170168239777687 chr22 51304566 1322520 0.02577782258210702 0.17307935551494164 chrMT 16571 12076 0.7287429847323638 0.9031341375636127 chrX 155270560 2959385 0.019059537107356347 0.16814676423532413 chrY 59373566 194526 0.0032763064963960563 0.0884500956021623