BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716745.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 = 1,227,059 number of mapped reads = 901,461 (73.47%) number of supplementary alignments = 939 (0.08%) number of secondary alignments = 0 number of mapped bases = 46,909,543 bp number of sequenced bases = 46,897,697 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,400 duplication rate = 7.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5546 >>>>>>> ACTG content number of A's = 9,931,955 bp (21.18%) number of C's = 8,537,771 bp (18.21%) number of T's = 15,376,169 bp (32.79%) number of G's = 13,050,933 bp (27.83%) number of N's = 869 bp (0%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 319,844 number of insertions = 2,382 mapped reads with insertion percentage = 0.26% number of deletions = 6,894 mapped reads with deletion percentage = 0.76% homopolymer indels = 39.86% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 0.1634X There is a 1.29% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 4594670 0.018433936018157404 0.1893736734835054 chr2 243199373 4030633 0.016573369208480647 0.24641487712073182 chr3 198022430 3122396 0.015767890536440746 0.14682416251402133 chr4 191154276 2878720 0.015059668348721637 0.150175993674157 chr5 180915260 2764299 0.015279523684182308 0.14273197029401172 chr6 171115067 2021353 0.011812828849256156 0.14533368493945029 chr7 159138663 2646992 0.016633242670890103 0.17067728464714796 chr8 146364022 2828621 0.019325931067950566 0.1658173737094422 chr9 141213431 2042657 0.014465033428725346 0.14710777196560762 chr10 135534747 2337274 0.017244832426624886 0.1760151313469757 chr11 135006516 1954778 0.014479138177301013 0.15240650719777854 chr12 133851895 2210866 0.01651725588195819 0.1509415511076137 chr13 115169878 790303 0.0068620633600046015 0.09574149637924916 chr14 107349540 2098025 0.01954386576784586 0.16505646852034725 chr15 102531392 906249 0.008838746673799181 0.1094539930513501 chr16 90354753 1261446 0.013961036449294483 0.15284845181567402 chr17 81195210 1842112 0.0226874467102185 0.18357705132211904 chr18 78077248 1250309 0.016013743209801656 0.16816719228654198 chr19 59128983 1270797 0.02149194752766169 0.20302292584298984 chr20 63025520 1239802 0.0196714283356964 0.17135698783950218 chr21 48129895 629429 0.013077713965509379 0.1401828877952732 chr22 51304566 535563 0.010438895438663295 0.12280876646468059 chrMT 16571 31152 1.8799106873453624 1.9741755246147419 chrX 155270560 1475617 0.009503520821976813 0.11631037791959362 chrY 59373566 145480 0.002450248651057947 0.07952183393876767