BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068160.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 = 3,954,178 number of mapped reads = 3,742,716 (94.65%) number of supplementary alignments = 33,316 (0.84%) number of secondary alignments = 0 number of mapped bases = 239,652,631 bp number of sequenced bases = 239,553,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 478,422 duplication rate = 10.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9362 >>>>>>> ACTG content number of A's = 61,967,176 bp (25.87%) number of C's = 43,414,137 bp (18.12%) number of T's = 77,657,379 bp (32.42%) number of G's = 56,487,047 bp (23.58%) number of N's = 27,370 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,305,833 number of insertions = 14,540 mapped reads with insertion percentage = 0.39% number of deletions = 56,994 mapped reads with deletion percentage = 1.51% homopolymer indels = 44.25% >>>>>>> Coverage mean coverageData = 0.0774X std coverageData = 0.7822X There is a 5.58% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.13% 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 0.01% 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 28329043 0.11365686025713051 1.4749279699213718 chr2 243199373 31531795 0.1296540965999941 1.4339817757564812 chr3 198022430 11333478 0.05723330432820161 0.3158587174436761 chr4 191154276 6989221 0.03656324695556379 0.28973552127513885 chr5 180915260 13393297 0.0740307755133536 0.36143828140062473 chr6 171115067 12630976 0.07381568567541746 0.5579302955292246 chr7 159138663 25838113 0.16236226013787736 1.389191737882723 chr8 146364022 8202119 0.05603917470920552 0.47006402863219676 chr9 141213431 10662252 0.0755045176970454 0.533066027023197 chr10 135534747 10343155 0.07631367770214674 0.5614992224238116 chr11 135006516 8220607 0.06089044620631496 0.3765566424015109 chr12 133851895 14801053 0.11057783679491426 0.4571514589143834 chr13 115169878 5107461 0.04434719467185682 0.3221887905334226 chr14 107349540 4690610 0.04369473776971937 0.3238696062109282 chr15 102531392 4923208 0.04801659183560095 0.3183969736197621 chr16 90354753 5554822 0.06147791693924502 0.3683546228373403 chr17 81195210 6216752 0.07656550183194304 0.377551265033963 chr18 78077248 3082605 0.03948147608891133 0.9395540089140151 chr19 59128983 2611656 0.04416879620608391 1.0400991085761881 chr20 63025520 4357696 0.06914176987353694 0.37185653427048443 chr21 48129895 4516736 0.09384470919789041 0.41934859910527544 chr22 51304566 2277265 0.04438717988570452 0.2717676612942368 chrMT 16571 530246 31.998430993905014 17.7823448074084 chrX 155270560 12983788 0.08362041072048687 0.435265189145641 chrY 59373566 524677 0.00883687868773117 0.2222068639328985