BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236102.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 = 1,889,532 number of mapped reads = 1,682,262 (89.03%) number of supplementary alignments = 8,807 (0.47%) number of secondary alignments = 0 number of mapped bases = 112,262,261 bp number of sequenced bases = 112,204,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,362 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.258 >>>>>>> ACTG content number of A's = 31,380,834 bp (27.97%) number of C's = 20,288,720 bp (18.08%) number of T's = 35,818,970 bp (31.92%) number of G's = 24,656,566 bp (21.97%) number of N's = 59,557 bp (0.05%) GC percentage = 40.06% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 933,520 number of insertions = 8,883 mapped reads with insertion percentage = 0.52% number of deletions = 32,548 mapped reads with deletion percentage = 1.91% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.3941X There is a 3.13% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% 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% 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 6371076 0.02556092327649607 0.611690224336194 chr2 243199373 4802846 0.019748595322242053 0.38235373357405045 chr3 198022430 8310935 0.04196966474959427 0.22820356197048916 chr4 191154276 5687124 0.029751487222812636 0.23281961602232276 chr5 180915260 7874116 0.04352378013883406 0.23639711638949018 chr6 171115067 11722330 0.06850553960861903 0.641444088511379 chr7 159138663 6937612 0.043594761129795344 0.4285450785154966 chr8 146364022 5928558 0.04050556905302862 0.6833931741077556 chr9 141213431 5468565 0.03872553029321977 0.4068276630269576 chr10 135534747 6974192 0.05145685629973545 0.41605901900361214 chr11 135006516 2351330 0.017416418626786872 0.2226928625312222 chr12 133851895 4962172 0.03707210869147575 0.22127079998485147 chr13 115169878 5903085 0.05125545934849388 0.25115404622080767 chr14 107349540 3383113 0.03151492777705429 0.22438091301990015 chr15 102531392 3049033 0.029737555889224637 0.19292931734895116 chr16 90354753 3329080 0.03684454762440666 0.2624684238827489 chr17 81195210 3164681 0.03897620315287072 0.25637784079984083 chr18 78077248 3406073 0.04362439874930018 0.6892873628654513 chr19 59128983 2604161 0.04404203941745455 0.41045151868874746 chr20 63025520 2309366 0.036641760353583755 0.2206156955656482 chr21 48129895 1597453 0.03319045262824696 0.24961236852873397 chr22 51304566 1781538 0.034724745551887135 0.2051357163212475 chrMT 16571 94060 5.676181280550359 4.020071767862987 chrX 155270560 3955950 0.025477785357378758 0.20985969545790636 chrY 59373566 293812 0.004948532146443756 0.17109970918293718