BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525084.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 = 1,016,873 number of mapped reads = 844,704 (83.07%) number of supplementary alignments = 2,838 (0.28%) number of secondary alignments = 0 number of mapped bases = 49,298,559 bp number of sequenced bases = 49,282,237 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,510 duplication rate = 5.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.969 >>>>>>> ACTG content number of A's = 12,172,391 bp (24.7%) number of C's = 9,644,313 bp (19.57%) number of T's = 16,244,977 bp (32.96%) number of G's = 11,215,519 bp (22.76%) number of N's = 5,037 bp (0.01%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 246,265 number of insertions = 3,617 mapped reads with insertion percentage = 0.43% number of deletions = 10,079 mapped reads with deletion percentage = 1.18% homopolymer indels = 43.68% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 0.1825X There is a 1.4% of reference with a coverageData >= 1X There is a 0.14% 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 3969395 0.015925316390686145 0.28731006832480055 chr2 243199373 4216063 0.017335830055778968 0.23002935391044 chr3 198022430 3211441 0.016217561818628323 0.1406326140577877 chr4 191154276 3230618 0.016900579299622888 0.18238831215510667 chr5 180915260 2913113 0.016102085584156912 0.14090600301656428 chr6 171115067 2762543 0.01614435857948149 0.1457697530493041 chr7 159138663 2650939 0.016658044940342374 0.1823306901800692 chr8 146364022 2494136 0.017040635846970645 0.201641228872055 chr9 141213431 2079655 0.014727034002877532 0.15382986204221052 chr10 135534747 2445394 0.01804256143998262 0.23186305388982556 chr11 135006516 2246746 0.016641759720693778 0.156900272987068 chr12 133851895 2189263 0.016355861080636924 0.143925996496166 chr13 115169878 1532552 0.01330688220404297 0.12780075782188724 chr14 107349540 1472524 0.013717096505490382 0.13042383241933805 chr15 102531392 1433344 0.013979562473900677 0.1311914359604289 chr16 90354753 1459773 0.016156017824541007 0.14535386219602076 chr17 81195210 1362067 0.016775213710266898 0.14824705108951847 chr18 78077248 1286192 0.0164733265188855 0.2109877389670749 chr19 59128983 1030716 0.017431654456157315 0.205948238412548 chr20 63025520 1102632 0.017495008371212168 0.15215361097006008 chr21 48129895 669146 0.013902918342123954 0.15835222305855334 chr22 51304566 622642 0.01213619076321589 0.12244296876055075 chrMT 16571 8696 0.5247721923842859 0.8097894276203208 chrX 155270560 2690287 0.017326446172410276 0.15451517608772286 chrY 59373566 218682 0.0036831542171477456 0.17493285592553512