BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365377.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 1,103,368,040 number of mapped reads = 1,067,313,091 (96.73%) number of supplementary alignments = 8,172,626 (0.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 537,159,897 number of mapped paired reads (second in pair) = 530,153,194 number of mapped paired reads (both in pair) = 1,058,517,910 number of mapped paired reads (singletons) = 8,795,181 number of mapped bases = 128,259,449,455 bp number of sequenced bases = 128,216,091,878 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 290,021,449 duplication rate = 23.05% >>>>>>> Insert size mean insert size = 74,014.7473 std insert size = 2,640,061.4352 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 54.0373 >>>>>>> ACTG content number of A's = 38,101,860,088 bp (29.72%) number of C's = 26,051,149,962 bp (20.32%) number of T's = 37,558,944,157 bp (29.29%) number of G's = 26,491,759,630 bp (20.66%) number of N's = 12,378,041 bp (0.01%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 686,849,744 number of insertions = 13,374,586 mapped reads with insertion percentage = 1.19% number of deletions = 16,205,031 mapped reads with deletion percentage = 1.46% homopolymer indels = 40.72% >>>>>>> Coverage mean coverageData = 41.4316X std coverageData = 541.169X There is a 92.35% of reference with a coverageData >= 1X There is a 92.33% of reference with a coverageData >= 2X There is a 92.3% of reference with a coverageData >= 3X There is a 92.28% of reference with a coverageData >= 4X There is a 92.25% of reference with a coverageData >= 5X There is a 92.21% of reference with a coverageData >= 6X There is a 92.17% of reference with a coverageData >= 7X There is a 92.12% of reference with a coverageData >= 8X There is a 92.05% of reference with a coverageData >= 9X There is a 91.96% of reference with a coverageData >= 10X There is a 91.85% of reference with a coverageData >= 11X There is a 91.71% of reference with a coverageData >= 12X There is a 91.53% of reference with a coverageData >= 13X There is a 91.31% of reference with a coverageData >= 14X There is a 91.04% of reference with a coverageData >= 15X There is a 90.71% of reference with a coverageData >= 16X There is a 90.33% of reference with a coverageData >= 17X There is a 89.89% of reference with a coverageData >= 18X There is a 89.4% of reference with a coverageData >= 19X There is a 88.86% of reference with a coverageData >= 20X There is a 88.28% of reference with a coverageData >= 21X There is a 87.65% of reference with a coverageData >= 22X There is a 86.99% of reference with a coverageData >= 23X There is a 86.29% of reference with a coverageData >= 24X There is a 85.56% of reference with a coverageData >= 25X There is a 84.77% of reference with a coverageData >= 26X There is a 83.92% of reference with a coverageData >= 27X There is a 83% of reference with a coverageData >= 28X There is a 81.97% of reference with a coverageData >= 29X There is a 80.82% of reference with a coverageData >= 30X There is a 79.53% of reference with a coverageData >= 31X There is a 78.06% of reference with a coverageData >= 32X There is a 76.38% of reference with a coverageData >= 33X There is a 74.49% of reference with a coverageData >= 34X There is a 72.36% of reference with a coverageData >= 35X There is a 69.97% of reference with a coverageData >= 36X There is a 67.35% of reference with a coverageData >= 37X There is a 64.47% of reference with a coverageData >= 38X There is a 61.38% of reference with a coverageData >= 39X There is a 58.08% of reference with a coverageData >= 40X There is a 54.61% of reference with a coverageData >= 41X There is a 51.01% of reference with a coverageData >= 42X There is a 47.31% of reference with a coverageData >= 43X There is a 43.58% of reference with a coverageData >= 44X There is a 39.85% of reference with a coverageData >= 45X There is a 36.17% of reference with a coverageData >= 46X There is a 32.59% of reference with a coverageData >= 47X There is a 29.15% of reference with a coverageData >= 48X There is a 25.87% of reference with a coverageData >= 49X There is a 22.8% of reference with a coverageData >= 50X There is a 19.94% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10634124742 42.66438614810914 1392.8114941479446 chr2 243199373 11086500742 45.58605807754282 289.4805396671184 chr3 198022430 8575498464 43.30569251170183 63.540291029152016 chr4 191154276 8738914595 45.7165530265198 391.01155112492137 chr5 180915260 7831450987 43.28795142543531 34.46504821755746 chr6 171115067 7463822244 43.618731972912705 166.79979187222094 chr7 159138663 7023914799 44.1370730819826 346.0991898691446 chr8 146364022 6575298309 44.92428001876035 469.14272408064335 chr9 141213431 5469222461 38.730186089735334 487.1049190899011 chr10 135534747 6990372706 51.576240489828045 1173.2595699151052 chr11 135006516 5940469581 44.00135457906343 291.32644309713146 chr12 133851895 5717995381 42.71882277796665 64.58771852701724 chr13 115169878 4154791713 36.07533310923539 20.506955902332944 chr14 107349540 3897204051 36.303872853111436 33.88389153662748 chr15 102531392 3556487500 34.68681572176451 29.483546708357753 chr16 90354753 3789374211 41.93884754463332 167.82251163568293 chr17 81195210 3526454402 43.43180345244504 238.3604832195518 chr18 78077248 3611568173 46.25634567704026 539.0822198350355 chr19 59128983 2517365049 42.57413067632163 625.4390369718295 chr20 63025520 2668171607 42.33478132350197 111.53281234430018 chr21 48129895 1818609109 37.78543686829153 188.86087156924944 chr22 51304566 1570136183 30.604219183922147 126.91912936714893 chrMT 16571 231270794 13956.357129925775 1124.3539377335057 chrX 155270560 3481189100 22.420149061096964 110.38241621072322 chrY 59373566 1389242552 23.39833440356269 616.0235622336415