BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238520.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 = 1,470,432 number of mapped reads = 1,315,883 (89.49%) number of supplementary alignments = 9,469 (0.64%) number of secondary alignments = 0 number of mapped bases = 81,574,359 bp number of sequenced bases = 81,539,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 351,618 duplication rate = 18.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1444 >>>>>>> ACTG content number of A's = 20,481,004 bp (25.12%) number of C's = 14,059,044 bp (17.24%) number of T's = 27,801,443 bp (34.1%) number of G's = 19,192,820 bp (23.54%) number of N's = 5,504 bp (0.01%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 456,041 number of insertions = 5,385 mapped reads with insertion percentage = 0.41% number of deletions = 20,223 mapped reads with deletion percentage = 1.52% homopolymer indels = 43.59% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.3991X There is a 1.32% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 7469853 0.029969245292271508 0.4831871805199938 chr2 243199373 8590248 0.03532183448515716 0.7106511117740941 chr3 198022430 3775257 0.01906479483157539 0.2631730569098215 chr4 191154276 4678460 0.024474786010018422 0.28074406499240456 chr5 180915260 3486492 0.019271409166921574 0.2550532331978059 chr6 171115067 7351630 0.04296307817242067 0.4459905676567796 chr7 159138663 5747287 0.03611496346428397 0.4769630391932024 chr8 146364022 3403518 0.023253788420763675 0.3258487454510325 chr9 141213431 3685668 0.026099981948600907 0.3882916936355261 chr10 135534747 3193577 0.023562791613873008 0.38113664811561276 chr11 135006516 1703635 0.0126189094458226 0.2022147165114695 chr12 133851895 2179791 0.0162850962999067 0.23579780184707663 chr13 115169878 2176996 0.018902477260590654 0.28371893774763407 chr14 107349540 1791091 0.01668466394918879 0.2412629603839423 chr15 102531392 2166877 0.0211337909076666 0.29527937270319726 chr16 90354753 2780688 0.030775226622555208 0.334312865714044 chr17 81195210 1470875 0.018115292761728186 0.23694041917345457 chr18 78077248 2444019 0.0313025761358802 0.6673324158098511 chr19 59128983 815546 0.013792660699068678 0.3431701736428943 chr20 63025520 1444615 0.02292111195591881 0.37401440686631887 chr21 48129895 927778 0.019276543196281647 0.26382279124199615 chr22 51304566 1962190 0.03824591362881814 0.36731980012494425 chrMT 16571 70661 4.264136141451934 4.243806260254166 chrX 155270560 8039237 0.05177566822712561 0.43906588921570744 chrY 59373566 218370 0.0036778993533923836 0.1313929891290855