BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238500.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 = 2,297,535 number of mapped reads = 2,060,537 (89.68%) number of supplementary alignments = 14,083 (0.61%) number of secondary alignments = 0 number of mapped bases = 127,542,828 bp number of sequenced bases = 127,465,124 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 362,463 duplication rate = 13.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9389 >>>>>>> ACTG content number of A's = 31,259,772 bp (24.52%) number of C's = 22,948,337 bp (18%) number of T's = 42,194,622 bp (33.1%) number of G's = 31,053,122 bp (24.36%) number of N's = 9,271 bp (0.01%) GC percentage = 42.37% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 813,497 number of insertions = 8,661 mapped reads with insertion percentage = 0.42% number of deletions = 45,243 mapped reads with deletion percentage = 2.17% homopolymer indels = 41.11% >>>>>>> Coverage mean coverageData = 0.0412X std coverageData = 0.555X There is a 2.7% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% 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% 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 7616584 0.030557933895779543 0.5119852540229032 chr2 243199373 13720568 0.05641695466048755 1.3461609045277836 chr3 198022430 9520940 0.04808010890483467 0.32383979958339915 chr4 191154276 7276969 0.03806856509974174 0.2912122431532769 chr5 180915260 5093882 0.028156176543648114 0.2519277158326637 chr6 171115067 4032156 0.023564003279734565 0.4239561800919663 chr7 159138663 6671208 0.04192072419258669 0.5506357639389852 chr8 146364022 6624792 0.045262434780591096 0.5997821585918223 chr9 141213431 4919914 0.034840269549147915 0.4054852816093595 chr10 135534747 7763571 0.057281038049969576 0.42044553648473004 chr11 135006516 6814374 0.05047440821300803 0.39201730840728416 chr12 133851895 3628159 0.027105772391194015 0.2546362631890214 chr13 115169878 2963778 0.025733968390589074 0.33308897106663315 chr14 107349540 2703302 0.02518224111626375 0.2679314236655067 chr15 102531392 3075935 0.02999993406897275 0.31601263732527096 chr16 90354753 3120156 0.034532284095779665 0.30783817055278073 chr17 81195210 3581377 0.044108230029825654 0.32026931473141884 chr18 78077248 6184633 0.0792117186302468 1.0133401864715612 chr19 59128983 2679371 0.04531400447053182 0.47248927734795254 chr20 63025520 4233892 0.06717742273288661 0.4007328462567619 chr21 48129895 3261105 0.06775632899261468 0.4022228591704918 chr22 51304566 1693788 0.03301437146939319 0.2625779527036146 chrMT 16571 71454 4.311990827348983 3.742509753043759 chrX 155270560 9891953 0.06370784648422727 0.39706546253445674 chrY 59373566 398967 0.006719606499633187 0.21635192360816205