BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818748.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 = 379,262 number of mapped reads = 368,407 (97.14%) number of supplementary alignments = 2,746 (0.72%) number of secondary alignments = 0 number of mapped bases = 24,990,827 bp number of sequenced bases = 24,980,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,097 duplication rate = 20.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2924 >>>>>>> ACTG content number of A's = 6,866,718 bp (27.49%) number of C's = 5,474,590 bp (21.92%) number of T's = 7,041,588 bp (28.19%) number of G's = 5,595,932 bp (22.4%) number of N's = 1,465 bp (0.01%) GC percentage = 44.32% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 125,729 number of insertions = 2,457 mapped reads with insertion percentage = 0.66% number of deletions = 6,481 mapped reads with deletion percentage = 1.74% homopolymer indels = 42.48% >>>>>>> Coverage mean coverageData = 0.0081X std coverageData = 0.1445X There is a 0.59% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 2046770 0.008211694686209027 0.1815746200859895 chr2 243199373 2240600 0.009213017173362531 0.22028003704755572 chr3 198022430 1662153 0.008393761252197542 0.11880032148371372 chr4 191154276 1664652 0.008708421463718656 0.1338635869785136 chr5 180915260 1518584 0.00839389667847809 0.1222824661928229 chr6 171115067 1487784 0.008694640548514643 0.12943940950158717 chr7 159138663 1374386 0.008636405346700694 0.13280952411571031 chr8 146364022 1281255 0.008753893084463065 0.12899226126700042 chr9 141213431 1078379 0.0076365186538099195 0.1253685250292337 chr10 135534747 1214038 0.008957393044014019 0.15118961436479433 chr11 135006516 1184279 0.008772013641178623 0.12891679529996264 chr12 133851895 1115692 0.008335272354567711 0.12034853427957197 chr13 115169878 797782 0.006927002214936791 0.10855872115336193 chr14 107349540 752131 0.00700637375809901 0.11251081435651993 chr15 102531392 710733 0.0069318575134530505 0.1104426727694854 chr16 90354753 742700 0.008219822149256498 0.17088721534615148 chr17 81195210 669747 0.00824860234981842 0.12260193563713377 chr18 78077248 666930 0.008541925043259721 0.15312346241338695 chr19 59128983 523972 0.00886150874605775 0.16590393620748387 chr20 63025520 531928 0.008439882764949818 0.12354310536900501 chr21 48129895 335157 0.0069635930018131145 0.11172900918854381 chr22 51304566 296852 0.005786073699561166 0.10442078118000717 chrMT 16571 44230 2.6691207531229257 3.1373215818606477 chrX 155270560 794092 0.005114247027897626 0.09777483798144836 chrY 59373566 256001 0.004311699923834792 0.22031868313129785