BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549012.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,042,107 number of mapped reads = 5,185,698 (85.83%) number of secondary alignments = 0 number of mapped bases = 204,805,168 bp number of sequenced bases = 204,780,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 423,563 duplication rate = 7.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4816 >>>>>>> ACTG content number of A's = 62,001,836 bp (30.28%) number of C's = 40,093,830 bp (19.58%) number of T's = 62,527,623 bp (30.53%) number of G's = 40,150,237 bp (19.61%) number of N's = 7,455 bp (0%) GC percentage = 39.19% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 543,147 number of insertions = 8,198 mapped reads with insertion percentage = 0.16% number of deletions = 18,746 mapped reads with deletion percentage = 0.36% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0662X std coverageData = 1.0748X There is a 3.69% of reference with a coverageData >= 1X There is a 1.51% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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% 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 15887297 0.0637402504204794 0.6267826453761661 chr2 243199373 17567007 0.07223294527161465 0.48942278077832996 chr3 198022430 14101635 0.07121231165580585 0.4344731593312257 chr4 191154276 13730480 0.07182931131501342 0.44578872957541077 chr5 180915260 12876182 0.07117244836063027 0.43597953386248983 chr6 171115067 12403171 0.07248438853137346 0.4436823755886531 chr7 159138663 11279649 0.07087937517735712 0.5627035243959415 chr8 146364022 10939954 0.07474483039281334 4.460101477564421 chr9 141213431 8358505 0.05919058081663634 0.4362223148275171 chr10 135534747 9387134 0.06925998098480236 0.4652887413260636 chr11 135006516 9364836 0.06936580749924692 0.5327501831625502 chr12 133851895 9189536 0.06865450802919151 0.4293169094699991 chr13 115169878 6985071 0.060650155416505695 0.4058499581947614 chr14 107349540 6182176 0.057589217429343434 0.4131099953021256 chr15 102531392 5826226 0.05682382620924526 0.3811523778942866 chr16 90354753 5274303 0.0583732767218123 0.3875348286957145 chr17 81195210 4937985 0.060816210709966755 0.40328464860640306 chr18 78077248 5377706 0.0688767360243025 0.643388431163039 chr19 59128983 3504481 0.05926841325851994 0.5590228469296983 chr20 63025520 3962878 0.06287735507775263 0.40675045244127916 chr21 48129895 2651868 0.05509814638074735 0.391237909989298 chr22 51304566 2096799 0.04086963721708512 0.4005201473796455 chrMT 16571 15968 0.9636111278739967 1.7126059031630987 chrX 155270560 12312986 0.07930019702382732 0.4929854153498002 chrY 59373566 591335 0.009959566855054655 0.16615211708103475