BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008814.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 = 2,719,648 number of mapped reads = 1,664,192 (61.19%) number of supplementary alignments = 7,745 (0.28%) number of secondary alignments = 0 number of mapped bases = 102,148,403 bp number of sequenced bases = 102,085,183 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,355 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0024 >>>>>>> ACTG content number of A's = 29,544,949 bp (28.94%) number of C's = 16,909,094 bp (16.56%) number of T's = 31,740,113 bp (31.09%) number of G's = 23,862,303 bp (23.37%) number of N's = 28,724 bp (0.03%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 1,186,255 number of insertions = 7,720 mapped reads with insertion percentage = 0.46% number of deletions = 41,726 mapped reads with deletion percentage = 2.48% homopolymer indels = 48.93% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.2717X There is a 2.72% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% 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% 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 9146771 0.03669708409673331 0.34981869695868256 chr2 243199373 8433975 0.034679262927211574 0.29215419315658075 chr3 198022430 8018048 0.04049060502893536 0.255012549139144 chr4 191154276 5991576 0.0313441902811528 0.2181932583343141 chr5 180915260 5848471 0.03232712928693798 0.22148038446524257 chr6 171115067 6512357 0.03805834935622589 0.28350973593908296 chr7 159138663 6262504 0.03935249851885459 0.413167343981424 chr8 146364022 9439709 0.06449473628157061 0.3707752533433611 chr9 141213431 2999269 0.021239261582703135 0.2145209238096047 chr10 135534747 5987198 0.04417463515831848 0.34683573195000783 chr11 135006516 4567343 0.03383053748309452 0.26398741408823656 chr12 133851895 4355402 0.03253896405426311 0.2237238710613796 chr13 115169878 3033069 0.02633561008026769 0.20676252850408688 chr14 107349540 3094573 0.02882707275690236 0.2117668823028708 chr15 102531392 2387333 0.023283922644881286 0.19408112948253212 chr16 90354753 2166876 0.02398187066041783 0.20353789736680786 chr17 81195210 2158837 0.02658823100525265 0.21462369077636004 chr18 78077248 2036881 0.026088022467185317 0.32546586520185206 chr19 59128983 1408641 0.023823190058925924 0.23459841666485282 chr20 63025520 1860388 0.02951801111676667 0.2118741552139148 chr21 48129895 965320 0.020056557364191218 0.181140695767652 chr22 51304566 914612 0.01782710724031853 0.15938297708082064 chrMT 16571 34902 2.1062096433528454 2.892290353904459 chrX 155270560 4310493 0.027761173785938557 0.21702743008926242 chrY 59373566 213855 0.003601855411547961 0.08008529747686516