BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525193.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 = 1,386,213 number of mapped reads = 1,268,980 (91.54%) number of supplementary alignments = 5,422 (0.39%) number of secondary alignments = 0 number of mapped bases = 72,934,114 bp number of sequenced bases = 72,914,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,299 duplication rate = 2.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5406 >>>>>>> ACTG content number of A's = 18,491,808 bp (25.36%) number of C's = 13,322,816 bp (18.27%) number of T's = 22,491,057 bp (30.85%) number of G's = 18,606,933 bp (25.52%) number of N's = 2,296 bp (0%) GC percentage = 43.79% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 358,494 number of insertions = 3,914 mapped reads with insertion percentage = 0.31% number of deletions = 11,499 mapped reads with deletion percentage = 0.9% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.0236X std coverageData = 0.2197X There is a 2.14% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 5778061 0.023181731611412917 0.3715092374245273 chr2 243199373 6269651 0.025779881430862076 0.22927859084418778 chr3 198022430 4981026 0.02515384747071329 0.1697931722410425 chr4 191154276 4790139 0.0250590209135578 0.18389925776000576 chr5 180915260 4446437 0.02457745687124458 0.16962989561682842 chr6 171115067 4199532 0.024542152094648686 0.18019762514275084 chr7 159138663 3961645 0.024894296114577764 0.2526207700372567 chr8 146364022 3718425 0.025405321261259137 0.2476838317215914 chr9 141213431 3035158 0.021493408796221372 0.20597486370364362 chr10 135534747 3407070 0.025137981775256495 0.21472849649634165 chr11 135006516 3286285 0.024341676960243905 0.2157678219604149 chr12 133851895 3301206 0.024663124866480226 0.17253496057786474 chr13 115169878 2336067 0.02028366305988446 0.15264969016914945 chr14 107349540 2333196 0.021734569146733187 0.16897035669628221 chr15 102531392 2111959 0.020598169583028778 0.15449087477929432 chr16 90354753 1996238 0.02209333691610003 0.16885854050223578 chr17 81195210 1876062 0.023105574823933578 0.17136166980427978 chr18 78077248 1993196 0.025528512480357913 0.33705953113686116 chr19 59128983 1397101 0.023628023502450565 0.2901468231723025 chr20 63025520 1524614 0.024190423180959077 0.17074561761886498 chr21 48129895 968865 0.020130212210103512 0.16688971948568504 chr22 51304566 818838 0.015960333822919386 0.13525923049860297 chrMT 16571 1867 0.11266670689759217 0.3372415997170266 chrX 155270560 4185050 0.026953274336100803 0.19591172000825272 chrY 59373566 216426 0.0036451575099935886 0.09143109470365468