BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716796.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 = 743,966 number of mapped reads = 557,431 (74.93%) number of supplementary alignments = 646 (0.09%) number of secondary alignments = 0 number of mapped bases = 29,255,486 bp number of sequenced bases = 29,247,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,695 duplication rate = 4.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3589 >>>>>>> ACTG content number of A's = 6,286,737 bp (21.49%) number of C's = 5,411,597 bp (18.5%) number of T's = 9,499,999 bp (32.48%) number of G's = 8,048,910 bp (27.52%) number of N's = 524 bp (0%) GC percentage = 46.02% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 196,534 number of insertions = 1,818 mapped reads with insertion percentage = 0.33% number of deletions = 4,513 mapped reads with deletion percentage = 0.8% homopolymer indels = 39.2% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.1174X There is a 0.85% 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 2868264 0.011507550065441963 0.13434760828745582 chr2 243199373 2495916 0.010262838958881691 0.16613197872170635 chr3 198022430 2021794 0.010209924198990993 0.11108859744598187 chr4 191154276 1861832 0.009739944295046793 0.11120040963656566 chr5 180915260 1805127 0.009977748698479056 0.10956520704108567 chr6 171115067 1276502 0.007459904159111833 0.10617288260660251 chr7 159138663 1672529 0.010509884703505395 0.11919592847277521 chr8 146364022 1868667 0.012767256423166617 0.12753685793452946 chr9 141213431 1305690 0.009246216813470102 0.10977018129698776 chr10 135534747 1493702 0.011020804871536005 0.12598443450162786 chr11 135006516 1271161 0.009415552950051686 0.11670816048951384 chr12 133851895 1292166 0.009653699710415008 0.10866932701810418 chr13 115169878 465791 0.00404438216041177 0.0718227166167927 chr14 107349540 888037 0.008272387566821433 0.10052495728260218 chr15 102531392 568084 0.005540586048027125 0.08179683920404913 chr16 90354753 827492 0.009158256456082614 0.10943864305621881 chr17 81195210 1201174 0.014793655931181163 0.13794049592223398 chr18 78077248 815012 0.010438533899145626 0.12076028336947547 chr19 59128983 680707 0.011512239268515747 0.1416570661236006 chr20 63025520 802650 0.012735317376199356 0.12706833125249598 chr21 48129895 399972 0.008310261221222278 0.1035372335677231 chr22 51304566 343909 0.006703282510956237 0.09422428312661824 chrMT 16571 8357 0.5043147667612093 0.8369040489259398 chrX 155270560 931671 0.006000306819270826 0.08613628119780381 chrY 59373566 89280 0.001503699474611311 0.05285226594526087