BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238597.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 = 2,741,213 number of mapped reads = 2,526,217 (92.16%) number of supplementary alignments = 21,871 (0.8%) number of secondary alignments = 0 number of mapped bases = 159,829,240 bp number of sequenced bases = 159,776,396 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 325,437 duplication rate = 10.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6856 >>>>>>> ACTG content number of A's = 41,114,918 bp (25.73%) number of C's = 28,831,794 bp (18.05%) number of T's = 52,081,238 bp (32.6%) number of G's = 37,739,936 bp (23.62%) number of N's = 8,510 bp (0.01%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 777,861 number of insertions = 9,808 mapped reads with insertion percentage = 0.38% number of deletions = 29,814 mapped reads with deletion percentage = 1.17% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.0516X std coverageData = 0.5841X There is a 3.81% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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% 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 13614912 0.05462338246290668 1.2938009375927422 chr2 243199373 16004215 0.06580697475729101 0.8876413310814742 chr3 198022430 10857057 0.05482741020802542 0.30313770791144395 chr4 191154276 12143656 0.06352803742669089 0.3346550252237913 chr5 180915260 9213115 0.05092502976255292 0.29386221798597956 chr6 171115067 8651812 0.05056136874259004 0.41764117169551623 chr7 159138663 8552718 0.053743809573164505 0.6181611866499602 chr8 146364022 7101302 0.04851808458775477 0.5474369830865448 chr9 141213431 6556285 0.04642819704593113 0.41763611594442734 chr10 135534747 7675883 0.0566340600466093 0.481893405729632 chr11 135006516 6325106 0.04685037572556868 0.3546715456205411 chr12 133851895 7377715 0.055118494960418755 0.31559690659152323 chr13 115169878 4203802 0.03650088089873638 0.27896629541401274 chr14 107349540 4434525 0.04130921287599369 0.2790061036019604 chr15 102531392 4597680 0.04484168126772335 0.31361301611261794 chr16 90354753 4628265 0.051223259942949545 0.32725595834868487 chr17 81195210 4343338 0.05349253976927949 0.34552648086174215 chr18 78077248 4380539 0.056105192129722606 0.8246709144143133 chr19 59128983 2975076 0.050315020638863346 0.8101368468921504 chr20 63025520 2794105 0.04433291466694761 0.28227481506188956 chr21 48129895 2264537 0.04705052857480782 0.29185979839287707 chr22 51304566 1418521 0.027649020556961734 0.2139981985262553 chrMT 16571 33842 2.0422424717880636 1.9997701909114025 chrX 155270560 9268388 0.059691856588911636 0.3481264478150318 chrY 59373566 412846 0.006953363724186618 0.17216899612519773