BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090211.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 27,391,670 number of mapped reads = 23,685,850 (86.47%) number of supplementary alignments = 1,243 (0%) number of secondary alignments = 0 number of mapped bases = 1,116,394,895 bp number of sequenced bases = 1,116,193,200 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,601,712 duplication rate = 12.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2286 >>>>>>> ACTG content number of A's = 325,669,721 bp (29.18%) number of C's = 229,986,676 bp (20.6%) number of T's = 319,824,888 bp (28.65%) number of G's = 240,709,374 bp (21.57%) number of N's = 2,541 bp (0%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 4,097,834 number of insertions = 39,162 mapped reads with insertion percentage = 0.17% number of deletions = 131,609 mapped reads with deletion percentage = 0.55% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.3606X std coverageData = 1.7531X There is a 15.06% of reference with a coverageData >= 1X There is a 7.75% of reference with a coverageData >= 2X There is a 4.47% of reference with a coverageData >= 3X There is a 2.74% of reference with a coverageData >= 4X There is a 1.75% of reference with a coverageData >= 5X There is a 1.15% of reference with a coverageData >= 6X There is a 0.77% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% 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 93045370 0.3733004540839238 2.660000678135754 chr2 243199373 104541166 0.42985787631944267 1.9775555105814595 chr3 198022430 108038517 0.545587270088545 1.5611601385578693 chr4 191154276 43306476 0.22655248371216138 0.9581660836739817 chr5 180915260 42901269 0.23713460655557744 0.959769103858215 chr6 171115067 64232961 0.3753787560974978 1.354886197035725 chr7 159138663 86824845 0.5455923995038214 2.8435567824633385 chr8 146364022 102540191 0.7005833100158999 2.82385968099763 chr9 141213431 35816086 0.2536308745306245 1.5649117413273324 chr10 135534747 35432669 0.26142867260452407 1.4310975571578617 chr11 135006516 48571183 0.35976917588185153 1.686824820451621 chr12 133851895 43522543 0.32515447764112715 1.1764887883643695 chr13 115169878 35732833 0.3102619679774255 1.1172678782688656 chr14 107349540 42241199 0.3934921286108911 1.3113160164709587 chr15 102531392 24778390 0.24166637667417995 0.9781909048418541 chr16 90354753 24814853 0.274638048094714 1.1109715110071339 chr17 81195210 22722555 0.27985092962996216 1.2083902193319618 chr18 78077248 43362569 0.5553803458851418 2.588453315006076 chr19 59128983 16253967 0.27489001459740986 1.8735314532761818 chr20 63025520 29644543 0.4703577693607288 1.4655658465581913 chr21 48129895 16698308 0.3469425395588334 1.3098105332934047 chr22 51304566 9989735 0.19471434569780788 0.8946606822189233 chrMT 16571 762073 45.988353147064146 27.2205254738275 chrX 155270560 37909004 0.2441480471249669 1.1047754333345101 chrY 59373566 2711590 0.045669987212828014 1.127618328235084