BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716213.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 = 1,832,047 number of mapped reads = 1,621,749 (88.52%) number of supplementary alignments = 6,634 (0.36%) number of secondary alignments = 0 number of mapped bases = 91,597,286 bp number of sequenced bases = 91,571,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,288 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3987 >>>>>>> ACTG content number of A's = 22,126,748 bp (24.16%) number of C's = 19,081,535 bp (20.84%) number of T's = 28,797,591 bp (31.45%) number of G's = 21,563,822 bp (23.55%) number of N's = 1,970 bp (0%) GC percentage = 44.39% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 458,366 number of insertions = 5,389 mapped reads with insertion percentage = 0.33% number of deletions = 15,313 mapped reads with deletion percentage = 0.94% homopolymer indels = 40.87% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.2331X There is a 2.66% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% 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 10250482 0.04112520144934764 0.3298483496732499 chr2 243199373 7568519 0.031120635331572173 0.268823055154078 chr3 198022430 5938873 0.02999091062562963 0.18896393926492527 chr4 191154276 5752333 0.030092620057319566 0.2072099169031136 chr5 180915260 4626855 0.025574708291605696 0.17547476208816437 chr6 171115067 4772269 0.027889238999625907 0.19433249527705063 chr7 159138663 3941572 0.024768160833423616 0.20643436610755792 chr8 146364022 5771737 0.039434124049966324 0.24041113847582815 chr9 141213431 3348518 0.02371246117516966 0.24114312049115424 chr10 135534747 4405710 0.032506129221608386 0.26738743335989845 chr11 135006516 3830563 0.028373171262341144 0.24021105617200844 chr12 133851895 4092702 0.030576347088698295 0.1938515962638109 chr13 115169878 2812065 0.024416670824293135 0.16873446862750455 chr14 107349540 2482762 0.023127830822563377 0.17401897155520615 chr15 102531392 2625220 0.02560406085191938 0.17609065672416624 chr16 90354753 2704957 0.029937074809999204 0.20567612032015564 chr17 81195210 2175618 0.026794905758603247 0.183949312731209 chr18 78077248 2232127 0.028588699745154954 0.437213905949215 chr19 59128983 1827757 0.030911355265487994 0.2570100368618093 chr20 63025520 2778465 0.04408476122053416 0.23776216798127883 chr21 48129895 1176927 0.024453138740485512 0.1908370864259403 chr22 51304566 1121565 0.02186091974737687 0.16242759615601554 chrMT 16571 2128 0.128417114235713 0.37897692788111054 chrX 155270560 5090555 0.0327850624097704 0.22212005029049692 chrY 59373566 267007 0.004497068611307597 0.10484049706562212