BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716715.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 = 473,819 number of mapped reads = 429,422 (90.63%) number of supplementary alignments = 1,823 (0.38%) number of secondary alignments = 0 number of mapped bases = 24,442,490 bp number of sequenced bases = 24,436,240 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,727 duplication rate = 1.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4668 >>>>>>> ACTG content number of A's = 5,765,643 bp (23.59%) number of C's = 4,470,144 bp (18.29%) number of T's = 7,907,752 bp (32.36%) number of G's = 6,292,173 bp (25.75%) number of N's = 528 bp (0%) GC percentage = 44.04% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 117,997 number of insertions = 1,280 mapped reads with insertion percentage = 0.3% number of deletions = 3,662 mapped reads with deletion percentage = 0.85% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.0079X std coverageData = 0.0999X There is a 0.76% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 2047287 0.008213768903709171 0.12982057867384822 chr2 243199373 2185395 0.008986022344720436 0.10773949578468509 chr3 198022430 1596973 0.008064606620573235 0.09236919425073731 chr4 191154276 1614336 0.008445199520412507 0.0966510309474334 chr5 180915260 1505362 0.008320812738516365 0.09387026293350802 chr6 171115067 1378553 0.008056292319366594 0.09376113739476993 chr7 159138663 1273285 0.008001104043459257 0.10378258430792753 chr8 146364022 1174613 0.008025285066298602 0.09741059402854037 chr9 141213431 990075 0.007011195698516807 0.09507986032129657 chr10 135534747 1063424 0.00784613557437046 0.09912278051034525 chr11 135006516 1092466 0.008091950169279237 0.10054843598884494 chr12 133851895 1188276 0.008877543347443829 0.09707717364930397 chr13 115169878 762388 0.0066196822749087225 0.08322103233197768 chr14 107349540 699630 0.00651730785246029 0.0843189267934473 chr15 102531392 722989 0.00705139163623176 0.08628509679082355 chr16 90354753 751588 0.008318189968379417 0.09590179710075514 chr17 81195210 663707 0.008174213725169256 0.09428608756382025 chr18 78077248 640169 0.008199174745503326 0.1392168100287771 chr19 59128983 500721 0.008468283650337772 0.10457235122637613 chr20 63025520 536748 0.00851635972222046 0.09552727717499326 chr21 48129895 307613 0.006391308354194415 0.08478334668833125 chr22 51304566 308699 0.00601698881927975 0.0800571653030011 chrMT 16571 4271 0.25773942429545593 0.504293012852435 chrX 155270560 1360961 0.00876509365329783 0.09949624061688281 chrY 59373566 72961 0.0012288465206890219 0.042332015176458584