BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237329.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 = 3,278,603 number of mapped reads = 3,029,201 (92.39%) number of supplementary alignments = 21,138 (0.64%) number of secondary alignments = 0 number of mapped bases = 193,357,415 bp number of sequenced bases = 193,236,178 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,149 duplication rate = 8.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0804 >>>>>>> ACTG content number of A's = 52,044,227 bp (26.93%) number of C's = 33,558,900 bp (17.37%) number of T's = 64,077,762 bp (33.16%) number of G's = 43,533,229 bp (22.53%) number of N's = 22,060 bp (0.01%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,224,510 number of insertions = 14,795 mapped reads with insertion percentage = 0.48% number of deletions = 67,881 mapped reads with deletion percentage = 2.21% homopolymer indels = 42.59% >>>>>>> Coverage mean coverageData = 0.0625X std coverageData = 0.7948X There is a 4.73% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 11088725 0.04448825425393825 1.2303363483225984 chr2 243199373 10353278 0.04257115416165156 0.9678973874026862 chr3 198022430 17574012 0.08874758278645505 0.37332680734375057 chr4 191154276 9413575 0.04924595565939629 0.4225616594818835 chr5 180915260 9894698 0.05469244551288819 0.2981599002557725 chr6 171115067 22154562 0.12947171975218288 0.7427549552371855 chr7 159138663 10627856 0.06678362001822273 0.8694680296002636 chr8 146364022 14555813 0.09944939200973857 2.1376122486087783 chr9 141213431 8363319 0.059224671058378295 0.5432751113037271 chr10 135534747 8691439 0.0641270168158428 0.7287381502712811 chr11 135006516 7189263 0.053251229740644515 0.4136781719216163 chr12 133851895 6684739 0.04994131013236682 0.30138096644422047 chr13 115169878 8722158 0.07573297941671867 0.36305918370355356 chr14 107349540 6554497 0.06105752292930179 0.3192957421218764 chr15 102531392 6831775 0.06663105675967025 0.3418017582696908 chr16 90354753 4954905 0.05483834370063521 0.35455850661673516 chr17 81195210 3530117 0.04347691200010444 0.2984024451069826 chr18 78077248 5865848 0.07512877503059534 1.1407309762930462 chr19 59128983 3485648 0.058949906173762535 0.804908835322675 chr20 63025520 3408168 0.05407599969028419 0.31388017273188784 chr21 48129895 3212534 0.06674716410663269 0.4031458633410797 chr22 51304566 1600184 0.031189894482296174 0.2127628737407272 chrMT 16571 24573 1.4828917989258343 1.6731826671938668 chrX 155270560 7972529 0.051346043963517614 0.33607800708206675 chrY 59373566 603200 0.010159403260366743 0.3701859915672443