BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090158.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 = 16,227,727 number of mapped reads = 14,910,147 (91.88%) number of supplementary alignments = 99,483 (0.61%) number of secondary alignments = 0 number of mapped bases = 965,248,182 bp number of sequenced bases = 964,906,544 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,102,248 duplication rate = 13.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1056 >>>>>>> ACTG content number of A's = 251,902,448 bp (26.11%) number of C's = 175,836,123 bp (18.22%) number of T's = 305,133,824 bp (31.62%) number of G's = 231,460,343 bp (23.99%) number of N's = 573,806 bp (0.06%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 6,297,433 number of insertions = 61,357 mapped reads with insertion percentage = 0.41% number of deletions = 192,418 mapped reads with deletion percentage = 1.28% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.3118X std coverageData = 2.5131X There is a 14.01% of reference with a coverageData >= 1X There is a 6.94% of reference with a coverageData >= 2X There is a 3.77% of reference with a coverageData >= 3X There is a 2.15% of reference with a coverageData >= 4X There is a 1.27% of reference with a coverageData >= 5X There is a 0.78% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 0.01% 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 80446908 0.3227550955630317 5.021352337838659 chr2 243199373 93670662 0.38515996503000854 2.9201008219990197 chr3 198022430 90043565 0.4547139685135669 1.3449237478477396 chr4 191154276 50326369 0.2632761874497644 1.1831134433460992 chr5 180915260 43896795 0.24263732644775238 0.9451905581562978 chr6 171115067 53844380 0.31466767330313467 1.3545739292649819 chr7 159138663 72131542 0.45326220944812134 4.507060666411799 chr8 146364022 87148521 0.5954231088292996 4.0033948858299135 chr9 141213431 30804900 0.21814426419537955 1.8435115351064517 chr10 135534747 30280810 0.2234173204307527 2.199570175581703 chr11 135006516 43042112 0.3188150711184933 1.7807162692056557 chr12 133851895 34206778 0.2555569198329243 1.0355177696739828 chr13 115169878 29921123 0.2597999018458629 0.9432781474960538 chr14 107349540 35670306 0.3322818709796055 1.1821899021810707 chr15 102531392 24845570 0.2423215906402597 0.9538622759081679 chr16 90354753 19225542 0.21277842461702043 1.0157623621484346 chr17 81195210 18987479 0.233849743106767 1.221912661437797 chr18 78077248 31399713 0.40216213819421504 3.527705599863628 chr19 59128983 15829137 0.2677052131946866 2.681537498493414 chr20 63025520 23496426 0.3728081259781752 1.2750948757665514 chr21 48129895 14341258 0.2979698584424504 1.2445462388645445 chr22 51304566 7708077 0.1502415399050447 0.7216593059887366 chrMT 16571 1192773 71.97954257437692 36.53991118465608 chrX 155270560 30101497 0.19386480605209383 1.0670131403386656 chrY 59373566 2685939 0.045237959936581876 2.339965890765768