BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818967.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,958,320 number of mapped reads = 1,933,411 (98.73%) number of supplementary alignments = 31,813 (1.62%) number of secondary alignments = 0 number of mapped bases = 178,930,690 bp number of sequenced bases = 178,827,869 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 923,925 duplication rate = 40.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0559 >>>>>>> ACTG content number of A's = 51,108,905 bp (28.58%) number of C's = 38,217,990 bp (21.37%) number of T's = 51,250,553 bp (28.66%) number of G's = 38,241,270 bp (21.38%) number of N's = 9,151 bp (0.01%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,082,483 number of insertions = 27,903 mapped reads with insertion percentage = 1.41% number of deletions = 56,928 mapped reads with deletion percentage = 2.88% homopolymer indels = 41.34% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.6395X There is a 2.52% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% 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 18320985 0.07350427022607098 1.0474344024445639 chr2 243199373 14033645 0.05770428117016568 0.8464630502109157 chr3 198022430 9911052 0.05005014835945605 0.4199056802394112 chr4 191154276 10372043 0.0542600626940723 0.47507876073869065 chr5 180915260 9409491 0.052010488225260824 0.4343798245589616 chr6 171115067 7729301 0.045170195328269956 0.47248176942164033 chr7 159138663 9120188 0.05730969349667089 0.7839701114047145 chr8 146364022 17051512 0.11650070671056033 0.7187435873089777 chr9 141213431 7445532 0.052725381341382466 0.5827935159947991 chr10 135534747 9267668 0.06837853912104178 0.714391881690086 chr11 135006516 5949350 0.04406713228567427 0.4367362228171353 chr12 133851895 8618232 0.06438632788874599 0.4906863800902822 chr13 115169878 3575125 0.031042187958209004 0.33682553536635285 chr14 107349540 3813530 0.035524418642129255 0.3705318924220778 chr15 102531392 4634382 0.04519963993076384 0.41333474487857536 chr16 90354753 5574320 0.061693710789071605 0.6988200656260469 chr17 81195210 5803211 0.07147233192696958 0.5628193125590272 chr18 78077248 4268231 0.05466677052961703 0.6468610553626027 chr19 59128983 3667667 0.06202824425375285 1.101565925455609 chr20 63025520 4983331 0.07906846306067765 0.5701726365686285 chr21 48129895 2592453 0.0538636745415713 0.48307512374440986 chr22 51304566 1391608 0.02712444736400265 0.3378465632431316 chrMT 16571 19865 1.198781002956973 2.184598534845576 chrX 155270560 10806824 0.06959995507197243 0.5350339393525694 chrY 59373566 571144 0.00961949969452736 0.5265470023376955