BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926888.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 26,297,908 number of mapped reads = 22,933,588 (87.21%) number of supplementary alignments = 607,434 (2.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,536,735 number of mapped paired reads (second in pair) = 11,396,853 number of mapped paired reads (both in pair) = 22,474,094 number of mapped paired reads (singletons) = 459,494 number of mapped bases = 2,074,980,749 bp number of sequenced bases = 2,073,368,917 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,016,661 duplication rate = 7.08% >>>>>>> Insert size mean insert size = 292,778.6652 std insert size = 5,190,681.9406 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 47.4996 >>>>>>> ACTG content number of A's = 584,860,349 bp (28.21%) number of C's = 407,872,261 bp (19.67%) number of T's = 594,103,584 bp (28.65%) number of G's = 486,362,453 bp (23.46%) number of N's = 170,270 bp (0.01%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 21,644,258 number of insertions = 357,200 mapped reads with insertion percentage = 1.53% number of deletions = 1,095,082 mapped reads with deletion percentage = 4.65% homopolymer indels = 51.74% >>>>>>> Coverage mean coverageData = 0.6703X std coverageData = 2.3245X There is a 27.96% of reference with a coverageData >= 1X There is a 14.81% of reference with a coverageData >= 2X There is a 8.31% of reference with a coverageData >= 3X There is a 5.04% of reference with a coverageData >= 4X There is a 3.19% of reference with a coverageData >= 5X There is a 2.09% of reference with a coverageData >= 6X There is a 1.4% of reference with a coverageData >= 7X There is a 0.97% of reference with a coverageData >= 8X There is a 0.68% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 199745484 0.8013840976548661 2.4521083825740617 chr2 243199373 8867568 0.03646213347762208 2.023470486834169 chr3 198022430 162938697 0.8228294996682951 1.729388120338143 chr4 191154276 143585665 0.7511506831267536 1.9231889721817874 chr5 180915260 144444945 0.7984121682162135 1.6708930129062556 chr6 171115067 3411085 0.01993445147644421 0.3236682082338452 chr7 159138663 123920097 0.7786925858488581 1.821595416635474 chr8 146364022 122489585 0.8368831583488462 1.8888684581662334 chr9 141213431 102379184 0.7249960805781994 2.5889003411639617 chr10 135534747 118497960 0.8742994886765089 6.192607819506937 chr11 135006516 115144740 0.8528828341885365 1.9920673794644144 chr12 133851895 109432355 0.81756298631409 1.8287924385936782 chr13 115169878 71904047 0.6243303218572481 1.4847718465529391 chr14 107349540 72213066 0.6726909682146751 1.5840153889998962 chr15 102531392 71699619 0.6992943097856313 1.6803709881451212 chr16 90354753 75866141 0.8396474837355817 3.2376921094022015 chr17 81195210 64956742 0.8000070693825412 1.8511241905230236 chr18 78077248 63235694 0.8099119221005331 2.396139053721618 chr19 59128983 41756901 0.706200223332101 1.8568299547715772 chr20 63025520 56565477 0.8975011550876534 1.918933271861018 chr21 48129895 30575642 0.6352733992043822 2.304922165683555 chr22 51304566 31534903 0.6146607496884391 1.6140507501024013 chrMT 16571 72751 4.390260092933438 3.7701622496183935 chrX 155270560 135988912 0.8758190348511656 1.8459080945930053 chrY 59373566 3753489 0.06321818366105886 1.5980101456756826