BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716368.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 = 1,850,026 number of mapped reads = 1,698,441 (91.81%) number of supplementary alignments = 30,980 (1.67%) number of secondary alignments = 0 number of mapped bases = 133,347,325 bp number of sequenced bases = 133,285,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,032 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3915 >>>>>>> ACTG content number of A's = 34,603,269 bp (25.96%) number of C's = 25,600,267 bp (19.21%) number of T's = 41,461,515 bp (31.11%) number of G's = 31,610,915 bp (23.72%) number of N's = 9,058 bp (0.01%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 931,923 number of insertions = 12,162 mapped reads with insertion percentage = 0.7% number of deletions = 32,794 mapped reads with deletion percentage = 1.9% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.0431X std coverageData = 0.3701X There is a 3.72% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10841593 0.04349675421671266 0.6404449406625017 chr2 243199373 11221389 0.04614069872622575 0.45101746746305477 chr3 198022430 8770042 0.044288124330157955 0.23419248931101183 chr4 191154276 8562447 0.04479338458533881 0.3003374083260918 chr5 180915260 8106127 0.0448062092716778 0.23806061881589483 chr6 171115067 7686133 0.04491792064108534 0.25760605257285524 chr7 159138663 7323658 0.04602060782677306 0.49851410168199356 chr8 146364022 6903139 0.04716417945934828 0.4687653500602229 chr9 141213431 5319240 0.037668088384595656 0.3528794580954137 chr10 135534747 6245682 0.04608177709587638 0.38245637898907703 chr11 135006516 6103196 0.045206677283635706 0.34865451536089687 chr12 133851895 5960897 0.04453352714954092 0.23719632540693908 chr13 115169878 4158550 0.03610796566095173 0.2108518699758794 chr14 107349540 4065560 0.037872169736358444 0.2349871390233512 chr15 102531392 3890587 0.03794532507663604 0.2172783815679694 chr16 90354753 3852575 0.042638321417358085 0.24760857327436167 chr17 81195210 3699761 0.045566247072949255 0.26969823488405364 chr18 78077248 3608566 0.04621789436021106 0.5330319351058839 chr19 59128983 2688337 0.04546563907584881 0.494522453461563 chr20 63025520 2881573 0.04572073344258008 0.253941955764292 chr21 48129895 1796222 0.03732029749909074 0.24837781571226752 chr22 51304566 1612958 0.03143887816924521 0.19991008603727167 chrMT 16571 10263 0.6193349828012793 0.9478198695267622 chrX 155270560 7628116 0.04912789649241943 0.2878747757484489 chrY 59373566 410714 0.006917455488524978 0.24287755946726008