BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124812.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 27,204,902 number of mapped reads = 26,937,230 (99.02%) number of supplementary alignments = 122,129 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,496,251 number of mapped paired reads (second in pair) = 13,440,979 number of mapped paired reads (both in pair) = 26,821,544 number of mapped paired reads (singletons) = 115,686 number of mapped bases = 2,334,734,548 bp number of sequenced bases = 2,333,480,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,495,500 duplication rate = 10.82% >>>>>>> Insert size mean insert size = 33,963.0145 std insert size = 1,698,988.884 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.6952 >>>>>>> ACTG content number of A's = 662,346,459 bp (28.38%) number of C's = 425,845,183 bp (18.25%) number of T's = 707,210,419 bp (30.31%) number of G's = 538,058,611 bp (23.06%) number of N's = 19,866 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 18,506,355 number of insertions = 308,844 mapped reads with insertion percentage = 1.12% number of deletions = 783,743 mapped reads with deletion percentage = 2.85% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.7542X std coverageData = 7.0596X There is a 31.4% of reference with a coverageData >= 1X There is a 16.3% of reference with a coverageData >= 2X There is a 8.92% of reference with a coverageData >= 3X There is a 5.25% of reference with a coverageData >= 4X There is a 3.22% of reference with a coverageData >= 5X There is a 2.05% of reference with a coverageData >= 6X There is a 1.35% of reference with a coverageData >= 7X There is a 0.92% of reference with a coverageData >= 8X There is a 0.64% of reference with a coverageData >= 9X There is a 0.46% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% 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 197704846 0.7931970047127787 10.757526192608191 chr2 243199373 208296519 0.8564846053283205 8.231565948402965 chr3 198022430 144401941 0.7292201242051216 1.6691820497715262 chr4 191154276 173150486 0.905815394890774 5.660392866798519 chr5 180915260 159008669 0.8789124201020965 1.8047375768763712 chr6 171115067 124395260 0.7269684790527534 7.127106984155814 chr7 159138663 102819437 0.6460996659246785 3.525866119261775 chr8 146364022 117297641 0.8014103424952342 3.212822721059655 chr9 141213431 118303303 0.8377624009432927 9.735120797689538 chr10 135534747 93887282 0.6927174328218578 14.417588307089646 chr11 135006516 117436390 0.8698572000776614 7.203296465204912 chr12 133851895 112259925 0.8386876031900781 1.8054630451294482 chr13 115169878 43600510 0.3785756376333055 0.9914181579339 chr14 107349540 75157892 0.7001230932149314 2.198044576886858 chr15 102531392 99486046 0.9702984038293365 2.0755094483782135 chr16 90354753 86731897 0.9599040904909563 11.32598262445388 chr17 81195210 41044406 0.5055027999804422 12.762548350235672 chr18 78077248 40216914 0.5150913362110304 9.81566471895958 chr19 59128983 29661786 0.5016454620909006 4.927175311795753 chr20 63025520 36630669 0.5812037568273931 1.9766742702278157 chr21 48129895 31347319 0.6513066151505214 3.1181519309841916 chr22 51304566 21672569 0.42242963326110194 1.3032782350061574 chrMT 16571 286799 17.307283809064028 12.05599114127387 chrX 155270560 153613673 0.989329033140603 4.310798253518719 chrY 59373566 6322369 0.1064845759811698 5.626066370760753