BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237844.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,935,871 number of mapped reads = 2,754,179 (69.98%) number of supplementary alignments = 15,225 (0.39%) number of secondary alignments = 0 number of mapped bases = 172,597,521 bp number of sequenced bases = 172,515,206 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,999 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.8856 >>>>>>> ACTG content number of A's = 46,130,555 bp (26.74%) number of C's = 34,214,042 bp (19.83%) number of T's = 50,591,906 bp (29.33%) number of G's = 41,423,477 bp (24.01%) number of N's = 155,226 bp (0.09%) GC percentage = 43.84% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,417,982 number of insertions = 14,591 mapped reads with insertion percentage = 0.53% number of deletions = 48,326 mapped reads with deletion percentage = 1.73% homopolymer indels = 43.9% >>>>>>> Coverage mean coverageData = 0.0558X std coverageData = 0.6015X There is a 4.62% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 17643967 0.07078805633146246 1.2428772198351468 chr2 243199373 10265044 0.04220834894997858 0.46898108305589276 chr3 198022430 9863967 0.04981237226510148 0.3058756097963872 chr4 191154276 2573115 0.013460933513200615 0.2900201992604005 chr5 180915260 9924009 0.054854460591107684 0.26936518937095233 chr6 171115067 12603134 0.07365297645005159 0.5311515526151509 chr7 159138663 13125248 0.08247680200756745 0.9591031076610976 chr8 146364022 7755170 0.05298549393511474 0.3532105782657477 chr9 141213431 9683079 0.06857052428674437 0.44481054740099985 chr10 135534747 11000184 0.08116135709464968 1.1804865165280995 chr11 135006516 10365456 0.07677744976398028 0.48857251635276516 chr12 133851895 10551312 0.0788282601452897 0.3290691828463939 chr13 115169878 12825969 0.11136565587053934 0.3875850337556086 chr14 107349540 4494423 0.04186718452636127 0.2879785155097303 chr15 102531392 3767867 0.03674842335116254 0.22327524526283424 chr16 90354753 2819387 0.031203527278747582 0.33410445824525664 chr17 81195210 2852009 0.035125335595535746 0.3459547039724574 chr18 78077248 1097830 0.014060818332121541 0.6320505653615044 chr19 59128983 2453309 0.04149080324956714 0.7593512754201193 chr20 63025520 2269803 0.03601403050700732 0.253793981218845 chr21 48129895 3428897 0.07124256140596193 0.38066733217311205 chr22 51304566 467038 0.009103244338915175 0.11383293637222422 chrMT 16571 56993 3.43932170659586 2.897733315285742 chrX 155270560 10079139 0.06491339375603462 0.36376958713183083 chrY 59373566 631172 0.0106305220070494 0.331129136516778