BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506323.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,160,676 number of mapped reads = 6,880,216 (84.31%) number of supplementary alignments = 75,340 (0.92%) number of secondary alignments = 0 number of mapped bases = 547,515,616 bp number of sequenced bases = 547,290,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,051,632 duplication rate = 11.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.913 >>>>>>> ACTG content number of A's = 148,734,728 bp (27.18%) number of C's = 104,584,969 bp (19.11%) number of T's = 156,128,409 bp (28.53%) number of G's = 137,709,792 bp (25.16%) number of N's = 132,340 bp (0.02%) GC percentage = 44.27% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 3,734,803 number of insertions = 43,238 mapped reads with insertion percentage = 0.61% number of deletions = 111,235 mapped reads with deletion percentage = 1.59% homopolymer indels = 43.1% >>>>>>> Coverage mean coverageData = 0.1769X std coverageData = 1.1517X There is a 9.91% of reference with a coverageData >= 1X There is a 3.8% of reference with a coverageData >= 2X There is a 1.69% of reference with a coverageData >= 3X There is a 0.83% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% 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 41505764 0.16652220898579026 1.791472945404709 chr2 243199373 43473477 0.17875653404747882 1.4040916609262593 chr3 198022430 34815750 0.17581720414197524 0.6777832959864822 chr4 191154276 33398875 0.1747220920132595 1.0668457328366503 chr5 180915260 40276153 0.2226244099032884 0.7830909881883069 chr6 171115067 19848902 0.11599739489918792 0.6071430285560292 chr7 159138663 27826642 0.17485783451630482 1.5111278855304564 chr8 146364022 33504059 0.2289091167500166 1.3884421435305243 chr9 141213431 15212877 0.107729674806924 1.1604427408154518 chr10 135534747 32532863 0.24003337682845272 1.4619860291238769 chr11 135006516 24167277 0.17900822653626586 1.1399241165948724 chr12 133851895 23738871 0.17735177376457764 0.7111019535109382 chr13 115169878 10837637 0.09410131527620443 0.4841373587397421 chr14 107349540 15745529 0.14667532809176453 0.7598913016339184 chr15 102531392 19979820 0.1948653930300683 0.7413181411549598 chr16 90354753 20698621 0.2290817064155994 0.9949470235494299 chr17 81195210 14069957 0.17328555465279294 0.8397127208736247 chr18 78077248 9667357 0.12381785023980353 1.6798741108883448 chr19 59128983 13976244 0.236368753374297 1.402171756304502 chr20 63025520 15742757 0.24978384946288423 0.9227051468618535 chr21 48129895 9501811 0.19742014812207673 0.9808558666931212 chr22 51304566 6675760 0.13012019242108003 0.6382220573056222 chrMT 16571 17487 1.0552772916540945 2.2006940171483413 chrX 155270560 38386964 0.24722628681187211 0.984937726115689 chrY 59373566 1914162 0.032239296524652065 1.0760893763581283