BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472835.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 3,393,210 number of mapped reads = 2,784,994 (82.08%) number of supplementary alignments = 20,971 (0.62%) number of secondary alignments = 0 number of mapped bases = 180,878,551 bp number of sequenced bases = 180,807,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,472 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4376 >>>>>>> ACTG content number of A's = 48,393,395 bp (26.77%) number of C's = 35,988,894 bp (19.9%) number of T's = 53,999,640 bp (29.87%) number of G's = 42,421,067 bp (23.46%) number of N's = 4,640 bp (0%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,534,388 number of insertions = 13,763 mapped reads with insertion percentage = 0.49% number of deletions = 39,742 mapped reads with deletion percentage = 1.41% homopolymer indels = 44.45% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.4153X There is a 4.95% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 13493357 0.05413570062880606 0.5894110740951465 chr2 243199373 17633641 0.07250693446483515 0.6304510557598133 chr3 198022430 12955759 0.06542571465262799 0.29004871289875556 chr4 191154276 10019009 0.05241320889939182 0.2958851108202742 chr5 180915260 9308336 0.05145135905064061 0.2599883764269639 chr6 171115067 10988147 0.06421495893169946 0.3178191062724297 chr7 159138663 11049205 0.06943130469809213 0.5216803139786796 chr8 146364022 10131768 0.06922307723956916 0.407787911767532 chr9 141213431 10326326 0.07312566465437696 0.4815456230702945 chr10 135534747 7576145 0.055898174952877584 0.3691582823519557 chr11 135006516 6169911 0.04570083861730052 0.4145698619466342 chr12 133851895 7450246 0.05566036999326756 0.27780459344267344 chr13 115169878 7167759 0.062236403515162186 0.2945668201932636 chr14 107349540 3684883 0.03432602505795553 0.2531837835983397 chr15 102531392 3502777 0.03416297127810378 0.22785401533205382 chr16 90354753 6142966 0.06798719266046802 0.3331245245703345 chr17 81195210 4098882 0.050481820294571565 0.28203636031716095 chr18 78077248 3084153 0.03950130260738698 0.7757018734122202 chr19 59128983 4222020 0.07140356193848287 0.4477435545603831 chr20 63025520 7746117 0.12290445203784119 0.4275311407411362 chr21 48129895 2271080 0.047186473188856944 0.30669522123710796 chr22 51304566 2145586 0.041820566224066685 0.2551817887879561 chrMT 16571 20906 1.2616015931446503 1.2664577733142028 chrX 155270560 8740347 0.056291076685754206 0.3135233782767185 chrY 59373566 949225 0.01598733348776794 0.20126409041282053