BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231830.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 = 4,757,763 number of mapped reads = 4,354,463 (91.52%) number of supplementary alignments = 23,345 (0.49%) number of secondary alignments = 0 number of mapped bases = 275,114,489 bp number of sequenced bases = 274,997,535 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 373,300 duplication rate = 6.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6184 >>>>>>> ACTG content number of A's = 67,669,998 bp (24.61%) number of C's = 51,109,540 bp (18.59%) number of T's = 87,284,187 bp (31.74%) number of G's = 68,831,980 bp (25.03%) number of N's = 101,830 bp (0.04%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 1,866,985 number of insertions = 19,967 mapped reads with insertion percentage = 0.45% number of deletions = 64,867 mapped reads with deletion percentage = 1.47% homopolymer indels = 43.71% >>>>>>> Coverage mean coverageData = 0.0889X std coverageData = 1.2465X There is a 7.04% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.25% 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 0.02% 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 0.01% 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 0.01% 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 25401615 0.1019119426787707 2.9054747569805897 chr2 243199373 19951543 0.08203780607608721 1.411315468900525 chr3 198022430 28360785 0.1432200635049272 0.47331347654011613 chr4 191154276 9305537 0.04868076819793453 0.3505916845464998 chr5 180915260 11972940 0.06617982363676785 0.34801726480536915 chr6 171115067 20857163 0.12188969309172523 0.9233925171684261 chr7 159138663 19593839 0.1231243158050159 2.4047911013725125 chr8 146364022 16363385 0.1117992302780529 0.8517152046114264 chr9 141213431 12607383 0.08927892276762257 0.831950161297272 chr10 135534747 12103464 0.08930155748178731 1.0370213645861273 chr11 135006516 9365370 0.06936976286389021 0.7454554179986428 chr12 133851895 9188548 0.0686471267366069 0.36931461672900784 chr13 115169878 7783287 0.06758092597788459 0.3415153465107648 chr14 107349540 11183480 0.1041781827849472 0.4906775320974291 chr15 102531392 5152107 0.05024906908510517 0.372645739741301 chr16 90354753 7757840 0.0858597886931305 0.5162123026875057 chr17 81195210 7458629 0.09186045580767634 0.4912470913023908 chr18 78077248 5526487 0.07078229755229078 1.9238843120078566 chr19 59128983 8831573 0.149361151704571 1.6336762069291075 chr20 63025520 7094243 0.11256143543123484 0.4675846715401571 chr21 48129895 4605902 0.09569732076082858 0.4360320666998813 chr22 51304566 3176955 0.061923435820507675 0.29908351185417226 chrMT 16571 160215 9.668396596463701 5.880977673554781 chrX 155270560 10554303 0.06797362616583595 0.5189007473612381 chrY 59373566 757896 0.012764872502352309 0.27542111795998186