BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082756.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,374,296 number of mapped reads = 2,694,148 (79.84%) number of supplementary alignments = 25,220 (0.75%) number of secondary alignments = 0 number of mapped bases = 180,105,274 bp number of sequenced bases = 180,035,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,059 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6989 >>>>>>> ACTG content number of A's = 50,953,967 bp (28.3%) number of C's = 32,731,305 bp (18.18%) number of T's = 57,718,347 bp (32.06%) number of G's = 38,622,771 bp (21.45%) number of N's = 9,400 bp (0.01%) GC percentage = 39.63% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,697,926 number of insertions = 16,171 mapped reads with insertion percentage = 0.59% number of deletions = 40,822 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.01% >>>>>>> Coverage mean coverageData = 0.0582X std coverageData = 0.4823X There is a 5.03% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% 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 15533475 0.06232070731731497 0.906691769018218 chr2 243199373 16803561 0.06909376777052793 0.5680315226615861 chr3 198022430 13272823 0.06702686660293988 0.2872145597611933 chr4 191154276 12291227 0.0643000368979452 0.2919341326221737 chr5 180915260 10242698 0.05661599800923372 0.26778834649567684 chr6 171115067 11938595 0.06976939675335544 0.41019775706287426 chr7 159138663 9678600 0.06081865850538156 0.4963703410796209 chr8 146364022 11861960 0.08104423367103153 0.7028162563564598 chr9 141213431 6441093 0.04561246727303156 0.4536849021552091 chr10 135534747 7378668 0.05444115375077949 0.36616706395418985 chr11 135006516 7647636 0.05664642142161494 0.3950331325497875 chr12 133851895 6821496 0.050963014008878996 0.2618062444436091 chr13 115169878 5008660 0.04348932278976626 0.23119686967961148 chr14 107349540 4718597 0.043955446851472305 0.2842872441683145 chr15 102531392 4053628 0.039535481972194426 0.22163939574714464 chr16 90354753 5929154 0.06562083125831798 0.3543323515218201 chr17 81195210 4354334 0.05362796647733284 0.3099969501046403 chr18 78077248 5127866 0.0656768281586974 1.0112107259772751 chr19 59128983 2760341 0.046683383680047395 0.624814196700388 chr20 63025520 3527205 0.055964710802862076 0.28483249517473735 chr21 48129895 3068788 0.06376053801904201 0.3038494168161361 chr22 51304566 2071650 0.040379446928758736 0.2234776469010237 chrMT 16571 152485 9.201919015146943 6.32815603783755 chrX 155270560 9025857 0.058129866988307376 0.31558959153501437 chrY 59373566 394877 0.006650720625404241 0.1410913070575977