BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525265.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 = 1,025,076 number of mapped reads = 942,013 (91.9%) number of supplementary alignments = 3,759 (0.37%) number of secondary alignments = 0 number of mapped bases = 54,876,448 bp number of sequenced bases = 54,858,221 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,538 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2907 >>>>>>> ACTG content number of A's = 13,724,992 bp (25.02%) number of C's = 10,009,671 bp (18.25%) number of T's = 17,897,153 bp (32.62%) number of G's = 13,225,132 bp (24.11%) number of N's = 1,273 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 276,698 number of insertions = 3,746 mapped reads with insertion percentage = 0.4% number of deletions = 11,294 mapped reads with deletion percentage = 1.19% homopolymer indels = 44.53% >>>>>>> Coverage mean coverageData = 0.0177X std coverageData = 0.2029X There is a 1.64% of reference with a coverageData >= 1X There is a 0.09% 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 5841700 0.023437052941184047 0.353974914958478 chr2 243199373 4569053 0.018787272942517003 0.2613064547543181 chr3 198022430 4375954 0.022098274422751 0.1573123789089507 chr4 191154276 3139914 0.016426072519560065 0.1404570482386958 chr5 180915260 2493932 0.013785083690563195 0.12418804692254297 chr6 171115067 3126948 0.01827394895623072 0.15491798100345516 chr7 159138663 4092019 0.025713543917357154 0.3467580175571545 chr8 146364022 3157606 0.021573648748187586 0.20329313081122863 chr9 141213431 1662292 0.011771486523827894 0.13567412641545182 chr10 135534747 2946246 0.021737938537635667 0.19659240219029062 chr11 135006516 2471313 0.018305138694194582 0.1625877095324947 chr12 133851895 2120967 0.01584562549525354 0.13454666830740622 chr13 115169878 1733619 0.015052711959979674 0.1293769453555527 chr14 107349540 2180403 0.02031124679248742 0.15198942812971025 chr15 102531392 1470297 0.014339969167686713 0.12779586289153225 chr16 90354753 1548489 0.0171378809480006 0.14616090110378674 chr17 81195210 987396 0.0121607666265042 0.11856709477936248 chr18 78077248 1195917 0.015317099803517665 0.25584874818972464 chr19 59128983 934371 0.01580225048010719 0.22627110625734412 chr20 63025520 976408 0.015492264086040068 0.1326219767556876 chr21 48129895 881570 0.018316474615205372 0.14651146872375348 chr22 51304566 434977 0.008478329199783115 0.09643963674276948 chrMT 16571 145121 8.757528211936515 5.470570287031562 chrX 155270560 2232302 0.014376852894714878 0.13419334532088242 chrY 59373566 157634 0.0026549525423485596 0.09041692642915426