BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084403.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,851,656 number of mapped reads = 2,620,779 (91.9%) number of supplementary alignments = 18,759 (0.66%) number of secondary alignments = 0 number of mapped bases = 176,881,272 bp number of sequenced bases = 176,819,335 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,847 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4046 >>>>>>> ACTG content number of A's = 50,416,340 bp (28.51%) number of C's = 33,287,839 bp (18.83%) number of T's = 55,266,610 bp (31.26%) number of G's = 37,613,886 bp (21.27%) number of N's = 234,660 bp (0.13%) GC percentage = 40.1% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,754,359 number of insertions = 12,769 mapped reads with insertion percentage = 0.48% number of deletions = 35,881 mapped reads with deletion percentage = 1.35% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 0.0571X std coverageData = 0.3733X There is a 4.74% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17443731 0.06998470427080701 0.5960245135536979 chr2 243199373 17212265 0.07077429841893548 0.42221840704402847 chr3 198022430 11978256 0.060489390015060415 0.29052546530563744 chr4 191154276 8717796 0.04560607370352521 0.2553536633351366 chr5 180915260 8728864 0.0482483567168408 0.253375958023331 chr6 171115067 8511707 0.049742592217200836 0.2902378452785687 chr7 159138663 10089331 0.06339962149864235 0.5313421009972904 chr8 146364022 8454932 0.05776646394699375 0.3937433873960322 chr9 141213431 6586621 0.04664302080444459 0.3114721802801379 chr10 135534747 12110137 0.0893507920887623 0.5071622543669916 chr11 135006516 9959885 0.07377336513150225 0.38410223330304943 chr12 133851895 9177087 0.0685615022484366 0.30583458885636644 chr13 115169878 4589946 0.03985370202441302 0.23043165171995583 chr14 107349540 4883417 0.04549080508402738 0.25616764500814787 chr15 102531392 3839260 0.037444727171947495 0.2295076889489335 chr16 90354753 3654044 0.04044108227488597 0.2547699176447863 chr17 81195210 4653518 0.05731271586094795 0.29708932257455656 chr18 78077248 4741862 0.06073295513694335 0.5644855097768354 chr19 59128983 3312545 0.05602235709009235 0.4240721505191176 chr20 63025520 3357505 0.05327215070974424 0.27240989050695325 chr21 48129895 1786184 0.03711173689450185 0.23163262296980208 chr22 51304566 1345895 0.026233435051375348 0.18484373942494875 chrMT 16571 21055 1.270593204996681 1.490878266485612 chrX 155270560 11367023 0.07320784442330858 0.33991557720296695 chrY 59373566 358406 0.0060364573689240765 0.12051876755541287