BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238275.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 = 2,023,153 number of mapped reads = 1,655,317 (81.82%) number of supplementary alignments = 17,672 (0.87%) number of secondary alignments = 0 number of mapped bases = 107,181,905 bp number of sequenced bases = 107,117,214 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,852 duplication rate = 7.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4081 >>>>>>> ACTG content number of A's = 29,383,024 bp (27.43%) number of C's = 20,301,646 bp (18.95%) number of T's = 33,236,441 bp (31.03%) number of G's = 24,170,099 bp (22.56%) number of N's = 26,004 bp (0.02%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,062,457 number of insertions = 8,989 mapped reads with insertion percentage = 0.54% number of deletions = 39,377 mapped reads with deletion percentage = 2.35% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.3408X There is a 2.28% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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% 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 8320598 0.033382456447320144 0.5039408162295431 chr2 243199373 8656766 0.035595346703463746 0.40086507569737573 chr3 198022430 7075002 0.03572828593205325 0.2684210073989437 chr4 191154276 7273411 0.03804995186191911 0.2888482339744588 chr5 180915260 7200322 0.039799417694228775 0.28389290691921226 chr6 171115067 6195644 0.03620747201647649 0.312559871773978 chr7 159138663 6400450 0.04021932746789509 0.4449217009104915 chr8 146364022 5523490 0.03773803100327484 0.40752010465674987 chr9 141213431 4701950 0.033296761977265464 0.31585573046992044 chr10 135534747 5130263 0.03785201296018946 0.34069408237249554 chr11 135006516 4274943 0.03166471609414764 0.29888865957144906 chr12 133851895 4519284 0.03376331728437614 0.26260596020936017 chr13 115169878 3588050 0.03115441348301159 0.2519907891021239 chr14 107349540 3365252 0.031348546067360886 0.27387541673506854 chr15 102531392 3015008 0.029405706303099834 0.2697682355238178 chr16 90354753 2840816 0.031440692444812506 0.26204018322638944 chr17 81195210 2941371 0.03622591776041961 0.29283471345645623 chr18 78077248 2677171 0.034288746959933836 0.48514741959708907 chr19 59128983 1931612 0.03266776971286653 0.38345509840052994 chr20 63025520 2473940 0.03925298831330547 0.28840713745266383 chr21 48129895 1659413 0.03447780220588472 0.2713912220008311 chr22 51304566 1340511 0.026128493124763983 0.22775897218347385 chrMT 16571 13696 0.8265041337275965 1.4694370388266493 chrX 155270560 5777537 0.03720948130798266 0.28962144462069994 chrY 59373566 285405 0.004806937147753598 0.1273123215928429