BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237582.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 = 2,370,995 number of mapped reads = 1,915,945 (80.81%) number of supplementary alignments = 10,718 (0.45%) number of secondary alignments = 0 number of mapped bases = 120,823,835 bp number of sequenced bases = 120,751,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,482 duplication rate = 4.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.1859 >>>>>>> ACTG content number of A's = 30,712,132 bp (25.43%) number of C's = 23,123,372 bp (19.15%) number of T's = 36,323,825 bp (30.08%) number of G's = 30,563,869 bp (25.31%) number of N's = 28,200 bp (0.02%) GC percentage = 44.46% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,150,278 number of insertions = 11,510 mapped reads with insertion percentage = 0.59% number of deletions = 43,614 mapped reads with deletion percentage = 2.24% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.039X std coverageData = 0.3743X There is a 2.97% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 10403883 0.041740650267025815 0.4560355827907841 chr2 243199373 10381630 0.04268773340957586 0.5366882151577954 chr3 198022430 8317514 0.04200288825866848 0.2938643196729817 chr4 191154276 7539186 0.03944032096880742 0.30335780004699664 chr5 180915260 6653770 0.03677837900462349 0.2616555697862725 chr6 171115067 6310266 0.03687732536141893 0.29075745013351123 chr7 159138663 7110928 0.044683849078209235 0.5475025917182333 chr8 146364022 6318067 0.0431668036561608 0.3535699912061871 chr9 141213431 4914409 0.034801286005153434 0.404070114222325 chr10 135534747 5274506 0.038916264033753645 0.3727657622250005 chr11 135006516 5038252 0.03731858394153361 0.4103600568872185 chr12 133851895 7115735 0.05316125707447026 0.3470940328166298 chr13 115169878 3913533 0.033980525706556707 0.2624126402591697 chr14 107349540 3398716 0.03166027539568404 0.2870569288003288 chr15 102531392 3791004 0.0369740810697274 0.28418245505269346 chr16 90354753 3409169 0.03773093154269372 0.32038201197749727 chr17 81195210 3130691 0.038557582399257294 0.2987067897769566 chr18 78077248 3100161 0.03970633032557705 0.5359597577658413 chr19 59128983 2553515 0.04318550515235481 0.3879903028407785 chr20 63025520 2520971 0.03999920984388546 0.2905420038375946 chr21 48129895 1471603 0.03057565365559181 0.2765882778985073 chr22 51304566 1431990 0.027911550796472968 0.241052697195648 chrMT 16571 110247 6.653008267455193 5.681212727211598 chrX 155270560 6162808 0.03969076945429964 0.3126996766252604 chrY 59373566 451281 0.007600705674306306 0.18239899436329043