BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231760.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 = 4,829,024 number of mapped reads = 4,285,886 (88.75%) number of supplementary alignments = 44,392 (0.92%) number of secondary alignments = 0 number of mapped bases = 282,729,315 bp number of sequenced bases = 282,605,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 359,573 duplication rate = 5.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5331 >>>>>>> ACTG content number of A's = 82,202,455 bp (29.09%) number of C's = 53,378,887 bp (18.89%) number of T's = 85,503,339 bp (30.26%) number of G's = 61,500,891 bp (21.76%) number of N's = 20,283 bp (0.01%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,697,408 number of insertions = 18,920 mapped reads with insertion percentage = 0.44% number of deletions = 72,485 mapped reads with deletion percentage = 1.67% homopolymer indels = 46.21% >>>>>>> Coverage mean coverageData = 0.0913X std coverageData = 5.5237X There is a 6.21% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 21356290 0.08568199314536512 2.1055440235470586 chr2 243199373 34820820 0.14317808294678458 19.462083386774932 chr3 198022430 51487826 0.26001007057634834 0.7029904838580379 chr4 191154276 7049579 0.03687900238234796 0.28659327833428844 chr5 180915260 14609668 0.08075420503499815 0.3874446425229141 chr6 171115067 23390909 0.13669695725859138 0.7084646720203044 chr7 159138663 17997642 0.11309408826690973 1.4644310158703082 chr8 146364022 18992053 0.1297590264361552 0.7844003607029495 chr9 141213431 9605058 0.06801802018392995 0.606327302633689 chr10 135534747 2108723 0.015558541604095075 0.6421745249737987 chr11 135006516 3607343 0.02671976958504729 0.4871866151535035 chr12 133851895 4062053 0.030347370128753128 0.27719661965449854 chr13 115169878 8853193 0.07687073350898227 0.3653313070005107 chr14 107349540 5321550 0.04957217329482735 0.3842474798722062 chr15 102531392 4455554 0.04345551067910987 0.28620146935201174 chr16 90354753 9502598 0.1051698741293665 0.5136208832934401 chr17 81195210 4477190 0.05514106066109072 0.31573318175888543 chr18 78077248 3676909 0.04709321978151689 1.4495689076171514 chr19 59128983 3443262 0.058233066514944115 1.2275930067405159 chr20 63025520 626576 0.009941623647055987 0.17842671680459177 chr21 48129895 3627344 0.07536571604820663 0.3925163192180575 chr22 51304566 3960636 0.07719850899820495 0.36959175912780506 chrMT 16571 323925 19.547703819926376 11.212052401808526 chrX 155270560 24547150 0.15809275113067153 0.6195553034694034 chrY 59373566 825464 0.013902887355628933 0.18277443131683982