BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236071.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 = 4,269,613 number of mapped reads = 3,791,725 (88.81%) number of supplementary alignments = 37,248 (0.87%) number of secondary alignments = 0 number of mapped bases = 243,435,213 bp number of sequenced bases = 243,304,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 286,582 duplication rate = 5.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2572 >>>>>>> ACTG content number of A's = 69,313,601 bp (28.49%) number of C's = 45,294,204 bp (18.62%) number of T's = 75,864,633 bp (31.18%) number of G's = 52,829,634 bp (21.71%) number of N's = 2,297 bp (0%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,890,739 number of insertions = 17,641 mapped reads with insertion percentage = 0.46% number of deletions = 76,050 mapped reads with deletion percentage = 1.98% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 0.0786X std coverageData = 0.7068X There is a 5.64% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 19391246 0.07779818530522337 1.1523653663182492 chr2 243199373 18627988 0.0765955428676208 0.7180591336161698 chr3 198022430 16631962 0.08399029342282084 0.3776443960781026 chr4 191154276 11827136 0.06187220211594953 0.374752180386972 chr5 180915260 11416200 0.06310247128959713 0.33305699390043514 chr6 171115067 26791170 0.15656815305457583 0.9877598399510155 chr7 159138663 15078194 0.09474877893123936 0.8553878532413567 chr8 146364022 17961210 0.12271601828487605 1.4985249486593322 chr9 141213431 10715283 0.07588005563011921 0.5956573856577076 chr10 135534747 8143485 0.060084112600291346 0.5640266555508615 chr11 135006516 10052484 0.07445925054461816 0.5309906363214556 chr12 133851895 9129010 0.0682023216780009 0.354758249394607 chr13 115169878 10903368 0.09467204610566662 0.4072945017274022 chr14 107349540 8953139 0.0834017453637901 0.42644803653486585 chr15 102531392 6454773 0.06295411457985473 0.3393908081578404 chr16 90354753 5262305 0.05824048901998548 0.37314153988491444 chr17 81195210 5440072 0.06699991292589796 0.3814629586951968 chr18 78077248 6823431 0.08739333384291413 1.0869338616586117 chr19 59128983 4080543 0.06901087745750675 0.7965686234711495 chr20 63025520 3612685 0.05732098680026757 0.32210056144027144 chr21 48129895 3828885 0.07955315506090342 0.41549642299133144 chr22 51304566 3095805 0.06034170525874832 0.31404214913510714 chrMT 16571 236265 14.257739424295456 9.616438904891837 chrX 155270560 8387816 0.054020646283493796 0.359683319886258 chrY 59373566 590758 0.009949848725609643 0.23372827229301602