BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038469.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 12,869,116 number of mapped reads = 12,114,824 (94.14%) number of supplementary alignments = 204,814 (1.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,120,674 number of mapped paired reads (second in pair) = 5,994,150 number of mapped paired reads (both in pair) = 11,969,240 number of mapped paired reads (singletons) = 145,584 number of mapped bases = 1,718,495,251 bp number of sequenced bases = 1,717,291,425 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,751,176 duplication rate = 8.85% >>>>>>> Insert size mean insert size = 78,557.2567 std insert size = 2,693,800.1627 median insert size = 259 >>>>>>> Mapping quality mean mapping quality = 53.6712 >>>>>>> ACTG content number of A's = 496,396,178 bp (28.91%) number of C's = 352,559,194 bp (20.53%) number of T's = 497,063,755 bp (28.94%) number of G's = 371,237,289 bp (21.62%) number of N's = 35,009 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 23,635,773 number of insertions = 302,903 mapped reads with insertion percentage = 2.37% number of deletions = 613,430 mapped reads with deletion percentage = 4.87% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.5551X std coverageData = 8.8807X There is a 24.6% of reference with a coverageData >= 1X There is a 12.53% of reference with a coverageData >= 2X There is a 6.23% of reference with a coverageData >= 3X There is a 3.44% of reference with a coverageData >= 4X There is a 1.88% of reference with a coverageData >= 5X There is a 1.07% of reference with a coverageData >= 6X There is a 0.62% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.23% 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 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% 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 0.02% 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 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 138639646 0.5562258799748386 15.065137653278054 chr2 243199373 156818777 0.6448157125799827 9.135839635381398 chr3 198022430 114963735 0.5805591568591497 1.3031702725173038 chr4 191154276 113289901 0.5926621332812874 6.9421955785538705 chr5 180915260 104547192 0.5778793452802157 1.3893325091337922 chr6 171115067 103720062 0.6061421931944777 12.238096117155717 chr7 159138663 90393150 0.568015014679368 7.377419159827133 chr8 146364022 87110468 0.5951631200733196 2.41971558726469 chr9 141213431 74932226 0.5306310134196796 15.828819844430464 chr10 135534747 95203251 0.702426891312233 16.389813311213494 chr11 135006516 81967618 0.6071382362018733 6.881777381113427 chr12 133851895 74564776 0.5570692592734678 1.302339009936719 chr13 115169878 51638090 0.44836454545866583 1.116030583091517 chr14 107349540 50046104 0.46619765673891106 1.2549034853636643 chr15 102531392 47417937 0.46247238114157274 1.1577720177751438 chr16 90354753 59653434 0.66021356950641 10.036629405115608 chr17 81195210 43828871 0.539796263843643 10.16880167852961 chr18 78077248 49784655 0.6376333218097031 12.977727838623595 chr19 59128983 24657566 0.417013193005535 7.741597402587667 chr20 63025520 36426022 0.5779567070608859 2.309998629740795 chr21 48129895 22229158 0.46185760430185857 3.004197481782211 chr22 51304566 17744921 0.3458741079692595 1.0329259358784855 chrMT 16571 5763626 347.814012431356 245.62246858831602 chrX 155270560 51786929 0.3335270317824577 1.9031621451702896 chrY 59373566 21367136 0.3598762452637593 8.968423738849403