BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524337.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 = 455,297 number of mapped reads = 414,924 (91.13%) number of supplementary alignments = 2,090 (0.46%) number of secondary alignments = 0 number of mapped bases = 24,091,619 bp number of sequenced bases = 24,085,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,030 duplication rate = 1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2539 >>>>>>> ACTG content number of A's = 5,759,494 bp (23.91%) number of C's = 4,534,365 bp (18.83%) number of T's = 7,707,294 bp (32%) number of G's = 6,080,517 bp (25.25%) number of N's = 3,410 bp (0.01%) GC percentage = 44.07% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 122,553 number of insertions = 1,356 mapped reads with insertion percentage = 0.32% number of deletions = 4,066 mapped reads with deletion percentage = 0.97% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.0078X std coverageData = 0.108X There is a 0.75% 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 2034295 0.008161644660456031 0.16667416634240678 chr2 243199373 1564257 0.006431994378538139 0.11725553187677915 chr3 198022430 1685939 0.008513878958055408 0.0944974455400573 chr4 191154276 1279365 0.006692840080647738 0.08553981632542668 chr5 180915260 1433739 0.007924920208499825 0.09101274117229241 chr6 171115067 1556474 0.009096066332954771 0.10032216921380104 chr7 159138663 1103551 0.006934524767246536 0.12211099827950815 chr8 146364022 2506235 0.017123299604324894 0.14735268947066163 chr9 141213431 990463 0.0070139433125167815 0.09458186198657274 chr10 135534747 1199930 0.00885330165555258 0.11202296374703594 chr11 135006516 1138025 0.008429407955390834 0.10326282771356209 chr12 133851895 952548 0.007116432681061408 0.08680791863554294 chr13 115169878 627681 0.005450044845927509 0.07553617005796756 chr14 107349540 516221 0.004808786325493337 0.07236295547995042 chr15 102531392 720984 0.007031836649598984 0.08632869388846598 chr16 90354753 726148 0.00803663311436422 0.09384671195630943 chr17 81195210 701045 0.008634068438273638 0.09741067498719977 chr18 78077248 576855 0.0073882598935864135 0.133533298613938 chr19 59128983 416517 0.007044210450905269 0.12356585331631324 chr20 63025520 514666 0.008165993711753588 0.0927891350817255 chr21 48129895 401768 0.008347576906203514 0.09510474044164056 chr22 51304566 168634 0.0032869199205388462 0.05867218259083773 chrMT 16571 13089 0.7898738760485184 0.9783579393824432 chrX 155270560 1196157 0.007703694763514732 0.09363983194728524 chrY 59373566 67033 0.0011290041093371416 0.04160261003559641