BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524399.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 = 681,136 number of mapped reads = 631,925 (92.78%) number of supplementary alignments = 2,242 (0.33%) number of secondary alignments = 0 number of mapped bases = 37,182,635 bp number of sequenced bases = 37,171,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,718 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9212 >>>>>>> ACTG content number of A's = 9,612,130 bp (25.86%) number of C's = 6,984,843 bp (18.79%) number of T's = 11,245,990 bp (30.25%) number of G's = 9,323,505 bp (25.08%) number of N's = 5,175 bp (0.01%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 180,263 number of insertions = 2,884 mapped reads with insertion percentage = 0.45% number of deletions = 6,875 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.86% >>>>>>> Coverage mean coverageData = 0.012X std coverageData = 0.1489X There is a 1.13% of reference with a coverageData >= 1X There is a 0.05% 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 3138294 0.01259091747659076 0.2658364251657637 chr2 243199373 3018940 0.012413436608654415 0.15861513707070343 chr3 198022430 2542498 0.012839444501312301 0.11701024220024298 chr4 191154276 2450876 0.012821455273121904 0.12347170210705546 chr5 180915260 2314506 0.012793315500306608 0.11750771200155677 chr6 171115067 1459155 0.008527332078828569 0.10001289995448254 chr7 159138663 2096451 0.01317373767303801 0.19086261920451983 chr8 146364022 1943415 0.01327795569870306 0.13821792526869728 chr9 141213431 1384876 0.009806970839763817 0.12334314913080932 chr10 135534747 1857802 0.013707200855290636 0.14257088987012403 chr11 135006516 1514300 0.011216495654180128 0.12518294632713642 chr12 133851895 1694773 0.012661554025813381 0.11863364343731468 chr13 115169878 1213508 0.010536678696490415 0.10628495766134365 chr14 107349540 1027149 0.00956826643132332 0.1031796801799144 chr15 102531392 1133490 0.011055053266028028 0.10906634940597762 chr16 90354753 1126848 0.012471374914831542 0.11814102184005323 chr17 81195210 968550 0.011928659338401858 0.11721307248342341 chr18 78077248 1038753 0.013304170249443218 0.17783124782808316 chr19 59128983 1023030 0.01730166744115995 0.19937891186240897 chr20 63025520 1035800 0.016434612518865375 0.13488002044635633 chr21 48129895 511349 0.010624353117745218 0.11219429610946811 chr22 51304566 253560 0.004942250169312415 0.07247609638649256 chrMT 16571 148319 8.950515961619697 5.56964425365038 chrX 155270560 2175818 0.014013074983435366 0.1295974193092823 chrY 59373566 110575 0.0018623607684268113 0.06334762489569136