BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777277.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 59,377,198 number of mapped reads = 57,712,533 (97.2%) number of supplementary alignments = 197,487 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,857,899 number of mapped paired reads (second in pair) = 28,854,634 number of mapped paired reads (both in pair) = 57,673,764 number of mapped paired reads (singletons) = 38,769 number of mapped bases = 5,736,855,472 bp number of sequenced bases = 5,733,935,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,448,626 duplication rate = 44.87% >>>>>>> Insert size mean insert size = 96,454.3023 std insert size = 3,205,281.8536 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 55.1183 >>>>>>> ACTG content number of A's = 1,371,374,836 bp (23.92%) number of C's = 1,480,354,248 bp (25.82%) number of T's = 1,374,740,375 bp (23.98%) number of G's = 1,507,252,900 bp (26.29%) number of N's = 213,420 bp (0%) GC percentage = 52.1% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 35,770,685 number of insertions = 594,767 mapped reads with insertion percentage = 1.02% number of deletions = 2,305,879 mapped reads with deletion percentage = 3.91% homopolymer indels = 55.39% >>>>>>> Coverage mean coverageData = 1.8532X std coverageData = 27.3911X There is a 11.48% of reference with a coverageData >= 1X There is a 6.48% of reference with a coverageData >= 2X There is a 4.33% of reference with a coverageData >= 3X There is a 3.41% of reference with a coverageData >= 4X There is a 2.86% of reference with a coverageData >= 5X There is a 2.52% of reference with a coverageData >= 6X There is a 2.27% of reference with a coverageData >= 7X There is a 2.1% of reference with a coverageData >= 8X There is a 1.96% of reference with a coverageData >= 9X There is a 1.84% of reference with a coverageData >= 10X There is a 1.75% of reference with a coverageData >= 11X There is a 1.66% of reference with a coverageData >= 12X There is a 1.59% of reference with a coverageData >= 13X There is a 1.53% of reference with a coverageData >= 14X There is a 1.47% of reference with a coverageData >= 15X There is a 1.42% of reference with a coverageData >= 16X There is a 1.38% of reference with a coverageData >= 17X There is a 1.33% of reference with a coverageData >= 18X There is a 1.29% of reference with a coverageData >= 19X There is a 1.26% of reference with a coverageData >= 20X There is a 1.22% of reference with a coverageData >= 21X There is a 1.19% of reference with a coverageData >= 22X There is a 1.16% of reference with a coverageData >= 23X There is a 1.13% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1.08% of reference with a coverageData >= 26X There is a 1.06% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 1.01% of reference with a coverageData >= 29X There is a 0.99% of reference with a coverageData >= 30X There is a 0.97% of reference with a coverageData >= 31X There is a 0.95% of reference with a coverageData >= 32X There is a 0.93% of reference with a coverageData >= 33X There is a 0.92% of reference with a coverageData >= 34X There is a 0.9% of reference with a coverageData >= 35X There is a 0.88% of reference with a coverageData >= 36X There is a 0.87% of reference with a coverageData >= 37X There is a 0.85% of reference with a coverageData >= 38X There is a 0.84% of reference with a coverageData >= 39X There is a 0.82% of reference with a coverageData >= 40X There is a 0.81% of reference with a coverageData >= 41X There is a 0.8% of reference with a coverageData >= 42X There is a 0.78% of reference with a coverageData >= 43X There is a 0.77% of reference with a coverageData >= 44X There is a 0.76% of reference with a coverageData >= 45X There is a 0.75% of reference with a coverageData >= 46X There is a 0.74% of reference with a coverageData >= 47X There is a 0.72% of reference with a coverageData >= 48X There is a 0.71% of reference with a coverageData >= 49X There is a 0.7% of reference with a coverageData >= 50X There is a 0.69% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 661671564 2.6546435926432457 32.592203510651046 chr2 243199373 403047695 1.6572727553865856 24.74569876239258 chr3 198022430 312536225 1.578286990014212 24.944040854652606 chr4 191154276 138470834 0.7243930760931553 15.378018257660864 chr5 180915260 218448611 1.2074637098053531 18.536329151619928 chr6 171115067 277789960 1.6234102868334792 26.831573916140822 chr7 159138663 322257085 2.025008121376513 31.806538505649073 chr8 146364022 130390645 0.8908654136328666 17.003533256754615 chr9 141213431 225177385 1.5945890090298847 23.303757624563133 chr10 135534747 220464594 1.6266278491669741 23.520945742138842 chr11 135006516 389111640 2.8821693317380324 34.316594451078394 chr12 133851895 334745915 2.5008679555862843 34.20410351736497 chr13 115169878 90488328 0.7856943983217556 14.573238464363508 chr14 107349540 126164215 1.1752655390977922 17.98362011331026 chr15 102531392 276631106 2.698013755631056 34.43553781611396 chr16 90354753 267954688 2.965584865247764 34.2954987696724 chr17 81195210 395772632 4.874334729844285 50.054060440089536 chr18 78077248 51368317 0.6579165930643457 11.994329930592375 chr19 59128983 345233983 5.838659240934349 51.27979910772675 chr20 63025520 226886534 3.599915304149811 43.08638163820496 chr21 48129895 41908017 0.8707273722496174 15.163623998321544 chr22 51304566 136402861 2.6586885268652307 30.936116220327747 chrMT 16571 53378 3.2211695130046465 3.8064094652304834 chrX 155270560 142893895 0.9202896865960939 17.317611651826518 chrY 59373566 985365 0.01659602187276405 0.8808124916988944