BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038477.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 16,955,116 number of mapped reads = 15,583,051 (91.91%) number of supplementary alignments = 219,687 (1.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,903,490 number of mapped paired reads (second in pair) = 7,679,561 number of mapped paired reads (both in pair) = 15,311,380 number of mapped paired reads (singletons) = 271,671 number of mapped bases = 2,098,035,632 bp number of sequenced bases = 2,096,601,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,091,620 duplication rate = 14.53% >>>>>>> Insert size mean insert size = 79,902.3776 std insert size = 2,757,019.7777 median insert size = 258 >>>>>>> Mapping quality mean mapping quality = 53.4347 >>>>>>> ACTG content number of A's = 597,688,213 bp (28.51%) number of C's = 418,032,492 bp (19.94%) number of T's = 607,135,721 bp (28.96%) number of G's = 473,581,925 bp (22.59%) number of N's = 163,142 bp (0.01%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 26,215,510 number of insertions = 360,192 mapped reads with insertion percentage = 2.2% number of deletions = 756,458 mapped reads with deletion percentage = 4.68% homopolymer indels = 48.27% >>>>>>> Coverage mean coverageData = 0.6777X std coverageData = 8.2494X There is a 26.04% of reference with a coverageData >= 1X There is a 14.89% of reference with a coverageData >= 2X There is a 8.49% of reference with a coverageData >= 3X There is a 5.26% of reference with a coverageData >= 4X There is a 3.25% of reference with a coverageData >= 5X There is a 2.09% of reference with a coverageData >= 6X There is a 1.36% of reference with a coverageData >= 7X There is a 0.9% of reference with a coverageData >= 8X There is a 0.61% of reference with a coverageData >= 9X There is a 0.42% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 183110067 0.7346423702591297 12.024456221084234 chr2 243199373 189756896 0.7802524063250772 9.575616516662624 chr3 198022430 133926490 0.6763197987217913 1.6358463936231797 chr4 191154276 89814542 0.46985369032498125 8.212105795836322 chr5 180915260 146415567 0.8093046822031486 1.7297974307379693 chr6 171115067 123345733 0.7208350215004737 6.960294743117113 chr7 159138663 102228745 0.6423878589453778 8.375049161693212 chr8 146364022 136152539 0.9302322875494635 3.470654823665267 chr9 141213431 89829070 0.6361227070532689 14.462444443950675 chr10 135534747 126473141 0.9331418237715824 19.204747690066537 chr11 135006516 96387172 0.7139445921262052 6.702289275883834 chr12 133851895 88385890 0.6603260267626394 1.6974820697075046 chr13 115169878 70960301 0.6161359396421345 1.4640953849942657 chr14 107349540 68956200 0.6423520771490963 1.5725548745851718 chr15 102531392 57554583 0.5613362100848099 1.4270718089010384 chr16 90354753 64288204 0.7115088234483913 7.742743024116636 chr17 81195210 51489202 0.6341408809706878 10.725549968846641 chr18 78077248 85168542 1.0908240772010818 9.790730719321221 chr19 59128983 27197072 0.4599617754291495 5.093176667741142 chr20 63025520 57657263 0.914824074438418 2.995777520835008 chr21 48129895 20156134 0.41878616190623313 3.7347419049546247 chr22 51304566 11957607 0.23307100970311298 0.8882883656586645 chrMT 16571 1986283 119.865005129443 72.32658973468675 chrX 155270560 70915754 0.45672376012555116 1.8820935440683912 chrY 59373566 3922635 0.06606702720197065 8.641434083608788