BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090159.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 = 21,877,082 number of mapped reads = 17,885,237 (81.75%) number of supplementary alignments = 1,004 (0%) number of secondary alignments = 0 number of mapped bases = 834,963,081 bp number of sequenced bases = 834,793,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,282,553 duplication rate = 9.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5292 >>>>>>> ACTG content number of A's = 270,295,869 bp (32.38%) number of C's = 163,509,411 bp (19.59%) number of T's = 221,754,251 bp (26.56%) number of G's = 179,139,114 bp (21.46%) number of N's = 94,548 bp (0.01%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 3,685,812 number of insertions = 35,533 mapped reads with insertion percentage = 0.2% number of deletions = 111,988 mapped reads with deletion percentage = 0.62% homopolymer indels = 45.07% >>>>>>> Coverage mean coverageData = 0.2697X std coverageData = 1.7503X There is a 14.1% of reference with a coverageData >= 1X There is a 5.52% of reference with a coverageData >= 2X There is a 2.64% of reference with a coverageData >= 3X There is a 1.43% of reference with a coverageData >= 4X There is a 0.85% of reference with a coverageData >= 5X There is a 0.54% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 69969030 0.2807175754238141 1.8613831675667785 chr2 243199373 91271550 0.3752951698604914 1.6070238468267186 chr3 198022430 79151544 0.3997099924488352 1.311374637670479 chr4 191154276 43711427 0.22867093488403054 0.9069156192394855 chr5 180915260 40580221 0.22430513047931944 0.8679640657222605 chr6 171115067 47762654 0.2791259404410016 1.0807422857835816 chr7 159138663 55733395 0.3502190727843428 2.454845312832286 chr8 146364022 69003713 0.4714526975761844 5.463290966149444 chr9 141213431 28180028 0.1995562872486258 1.0959248982155287 chr10 135534747 21009099 0.15500895132080042 0.9277988735244821 chr11 135006516 35580294 0.2635450128940443 1.1687950518437045 chr12 133851895 30370706 0.2268978410802477 0.8844783642895622 chr13 115169878 24699768 0.21446378540055414 0.861816874813917 chr14 107349540 29627189 0.2759880387004919 1.036950367232317 chr15 102531392 21950086 0.2140816151213474 0.8575647776296457 chr16 90354753 16070792 0.17786327189672024 0.7913170515472707 chr17 81195210 16606087 0.2045205252871444 0.8880088846628208 chr18 78077248 28161739 0.3606907226033377 1.6941895682974524 chr19 59128983 13916948 0.23536592875274043 1.456999116374064 chr20 63025520 20757043 0.32934346277507903 1.1227221731373245 chr21 48129895 12142904 0.2522944211700441 1.0662635738181265 chr22 51304566 6874133 0.1339867683511834 0.6426643260550804 chrMT 16571 1244950 75.1282360750709 54.951772721315166 chrX 155270560 28550065 0.18387300850850283 0.8598540440636387 chrY 59373566 2037716 0.03432025625679953 1.0952130517120486