BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238269.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 = 2,082,023 number of mapped reads = 1,867,631 (89.7%) number of supplementary alignments = 15,932 (0.77%) number of secondary alignments = 0 number of mapped bases = 123,227,961 bp number of sequenced bases = 123,161,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,661 duplication rate = 2.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4421 >>>>>>> ACTG content number of A's = 34,820,868 bp (28.27%) number of C's = 23,449,218 bp (19.04%) number of T's = 37,068,739 bp (30.1%) number of G's = 27,787,698 bp (22.56%) number of N's = 34,773 bp (0.03%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,132,922 number of insertions = 10,728 mapped reads with insertion percentage = 0.57% number of deletions = 39,320 mapped reads with deletion percentage = 2.08% homopolymer indels = 44.53% >>>>>>> Coverage mean coverageData = 0.0398X std coverageData = 0.3945X There is a 3.54% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 13248585 0.053153668973205885 0.7322539575911756 chr2 243199373 9558185 0.039301848857973824 0.497747378456298 chr3 198022430 7333147 0.037031900881127455 0.21221040049071188 chr4 191154276 7006096 0.03665152643511883 0.23509384358183613 chr5 180915260 7958309 0.04398915271160653 0.23020667280240753 chr6 171115067 7507804 0.04387576226703637 0.287809515512455 chr7 159138663 5291720 0.03325225875499532 0.4193370615703637 chr8 146364022 7201702 0.04920404551331611 0.4995347086154664 chr9 141213431 5345089 0.03785113754512487 0.40758096439440683 chr10 135534747 6025112 0.04445437154208138 0.4622848348654646 chr11 135006516 4879526 0.036142892540090434 0.2936857416490035 chr12 133851895 4951105 0.036989427755206604 0.21912855451344174 chr13 115169878 2205086 0.019146377840219646 0.1485424960331518 chr14 107349540 3305535 0.030792260497809306 0.25386844241529466 chr15 102531392 3293174 0.03211869004958013 0.19820520619032986 chr16 90354753 4071320 0.04505927872991917 0.29888800139516897 chr17 81195210 2466835 0.03038153359046673 0.22284211706521734 chr18 78077248 3959022 0.05070647469541959 0.7163141961634831 chr19 59128983 2360274 0.03991737858910917 0.5554462077731162 chr20 63025520 2501642 0.03969252455195927 0.22300856824720208 chr21 48129895 1285588 0.026710800013172685 0.21604739117639932 chr22 51304566 1575427 0.030707344839443724 0.1894238023719377 chrMT 16571 8313 0.5016595256773883 0.8036607210015669 chrX 155270560 9507662 0.06123286990141595 0.3236732329704553 chrY 59373566 381703 0.006428837371836483 0.18355801627432974