BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231863.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 = 2,124,255 number of mapped reads = 1,615,145 (76.03%) number of supplementary alignments = 12,372 (0.58%) number of secondary alignments = 0 number of mapped bases = 106,715,308 bp number of sequenced bases = 106,668,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,604 duplication rate = 5.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7526 >>>>>>> ACTG content number of A's = 28,905,690 bp (27.1%) number of C's = 20,348,318 bp (19.08%) number of T's = 33,199,728 bp (31.12%) number of G's = 24,208,733 bp (22.7%) number of N's = 5,546 bp (0.01%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 757,141 number of insertions = 7,828 mapped reads with insertion percentage = 0.48% number of deletions = 26,448 mapped reads with deletion percentage = 1.62% homopolymer indels = 45.93% >>>>>>> Coverage mean coverageData = 0.0345X std coverageData = 0.3474X There is a 2.58% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.15% 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% 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 8435785 0.0338445896991366 0.7212239465009702 chr2 243199373 8424349 0.03463968223306234 0.38569694782799485 chr3 198022430 5558685 0.02807098670589993 0.21309262203637874 chr4 191154276 7837825 0.04100261403516812 0.2714574609371461 chr5 180915260 6713466 0.03710834564204258 0.24461602502494395 chr6 171115067 5791964 0.033848357725272664 0.26863958598098103 chr7 159138663 6009184 0.03776067918831265 0.3440925106939978 chr8 146364022 4122866 0.02816857547136823 0.29286944221292854 chr9 141213431 4382810 0.031036778647492814 0.28178463911159596 chr10 135534747 6030645 0.044495195021834515 0.3835865816784219 chr11 135006516 6099356 0.04517823421204351 0.3084519571441401 chr12 133851895 4469468 0.03339114474247824 0.23619365690968228 chr13 115169878 3147911 0.027332763172676106 0.21033835992522618 chr14 107349540 3008448 0.028024787064760595 0.2253717262892474 chr15 102531392 2783352 0.02714633972783672 0.2112407165343387 chr16 90354753 3255547 0.03603072214695778 0.25991164273759526 chr17 81195210 3266702 0.040232693529581365 0.2718129201200803 chr18 78077248 2924406 0.0374552904323677 0.4352357168283421 chr19 59128983 2370782 0.04009509177588933 0.48133282416127876 chr20 63025520 2360952 0.03746025419544337 0.2540833024480126 chr21 48129895 1091955 0.022687666366195066 0.20547675858695416 chr22 51304566 1053517 0.020534566065718206 0.18515625164160318 chrMT 16571 25870 1.5611610645102891 1.5821517873262887 chrX 155270560 7199615 0.046368191111051574 0.29733193710518907 chrY 59373566 349848 0.00589231915091642 0.13261474774887383