BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524688.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 = 831,965 number of mapped reads = 770,767 (92.64%) number of supplementary alignments = 3,227 (0.39%) number of secondary alignments = 0 number of mapped bases = 45,834,063 bp number of sequenced bases = 45,820,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,493 duplication rate = 1.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9827 >>>>>>> ACTG content number of A's = 11,992,363 bp (26.17%) number of C's = 9,023,795 bp (19.69%) number of T's = 14,206,436 bp (31%) number of G's = 10,591,739 bp (23.12%) number of N's = 6,209 bp (0.01%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 225,402 number of insertions = 3,524 mapped reads with insertion percentage = 0.45% number of deletions = 8,618 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.45% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1646X There is a 1.38% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3621922 0.014531245641309757 0.2544119983777458 chr2 243199373 3817308 0.015696208229944737 0.2082945046360838 chr3 198022430 3062583 0.015465838895119103 0.13043045161534542 chr4 191154276 2983068 0.015605552030654024 0.14192441508440218 chr5 180915260 2728747 0.015083011792371743 0.12923204750815903 chr6 171115067 2596215 0.015172334298299986 0.13685417982860512 chr7 159138663 2542726 0.01597805305175902 0.1848665920379666 chr8 146364022 2331715 0.01593093007515194 0.18033924517419345 chr9 141213431 1957770 0.013863907888478398 0.148090079957668 chr10 135534747 2237253 0.016506859307451247 0.1732836385773314 chr11 135006516 2092537 0.015499525963620897 0.15487919949532206 chr12 133851895 2058880 0.015381777000616988 0.13072299950433577 chr13 115169878 1428766 0.012405726434823522 0.11693388915844595 chr14 107349540 1395480 0.012999403630420773 0.12355175520630046 chr15 102531392 1298612 0.012665506384620235 0.11855597851347897 chr16 90354753 1340781 0.014839075482835973 0.1333579379223645 chr17 81195210 1249139 0.015384392749276712 0.13325870952651156 chr18 78077248 1216735 0.015583733176661145 0.23512761077438935 chr19 59128983 959664 0.016230010247258946 0.20816878334783914 chr20 63025520 1003383 0.015920265314748692 0.13356956308051676 chr21 48129895 622790 0.012939774749144995 0.1305613008457797 chr22 51304566 548474 0.010690549453239698 0.10858702940892907 chrMT 16571 16113 0.9723613541729528 1.1373413915105317 chrX 155270560 2569590 0.016549112722978522 0.14108008555087465 chrY 59373566 153812 0.0025905804613453737 0.09853682191249614