BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237256.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 = 2,506,939 number of mapped reads = 2,238,868 (89.31%) number of supplementary alignments = 29,742 (1.19%) number of secondary alignments = 0 number of mapped bases = 134,285,126 bp number of sequenced bases = 134,207,761 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 631,704 duplication rate = 20.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6672 >>>>>>> ACTG content number of A's = 34,526,073 bp (25.73%) number of C's = 22,437,529 bp (16.72%) number of T's = 46,075,293 bp (34.33%) number of G's = 31,155,209 bp (23.21%) number of N's = 13,657 bp (0.01%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 911,185 number of insertions = 9,206 mapped reads with insertion percentage = 0.41% number of deletions = 45,425 mapped reads with deletion percentage = 2.01% homopolymer indels = 40.95% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.6309X There is a 2.05% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 10548220 0.042319734080020606 0.6840423790095362 chr2 243199373 11496528 0.04727202976793859 1.312507919372274 chr3 198022430 9367291 0.04730419175241916 0.4003614446829312 chr4 191154276 9422235 0.04929125938045979 0.44790917499441607 chr5 180915260 8654045 0.04783479845757622 0.40378229775028324 chr6 171115067 8220165 0.048038814723428185 0.5749954544795379 chr7 159138663 7564125 0.04753166111493597 0.5933701192493092 chr8 146364022 7301132 0.049883379127146424 0.8467455237648821 chr9 141213431 5725429 0.040544507413037785 0.43181649519940857 chr10 135534747 6602451 0.04871408362904901 0.5600860023125344 chr11 135006516 6255477 0.04633463024851334 0.4365350810960607 chr12 133851895 6130356 0.045799545833848675 0.39627588487204163 chr13 115169878 4555459 0.039554257407479414 0.42379677278751976 chr14 107349540 4162421 0.038774465172370556 0.3698171780300079 chr15 102531392 3699286 0.03607954527721617 0.37386046871083256 chr16 90354753 3496854 0.03870138408767494 0.3780777429578364 chr17 81195210 3180961 0.03917670759149462 0.3810665689375801 chr18 78077248 3911379 0.05009627132349747 1.2577687800524362 chr19 59128983 2261898 0.03825362597560658 0.5656028243227247 chr20 63025520 2569987 0.040776926552926494 0.37787677081795573 chr21 48129895 1798795 0.03737375699656108 0.3760172982558885 chr22 51304566 1232507 0.02402333936515514 0.2835145574681346 chrMT 16571 41825 2.5239876893367934 3.2801687465886507 chrX 155270560 4676197 0.03011644319438276 0.32310317014227924 chrY 59373566 1410103 0.023749676750087743 0.42262407418155085