BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084872.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 = 2,030,809 number of mapped reads = 1,748,992 (86.12%) number of supplementary alignments = 11,655 (0.57%) number of secondary alignments = 0 number of mapped bases = 120,999,147 bp number of sequenced bases = 120,952,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,288 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0755 >>>>>>> ACTG content number of A's = 35,206,031 bp (29.11%) number of C's = 22,253,123 bp (18.4%) number of T's = 38,302,519 bp (31.67%) number of G's = 25,171,487 bp (20.81%) number of N's = 19,282 bp (0.02%) GC percentage = 39.21% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,070,175 number of insertions = 10,465 mapped reads with insertion percentage = 0.59% number of deletions = 26,582 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.3933X There is a 3.46% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 9982534 0.040050187076565 0.8336301922669213 chr2 243199373 10911938 0.044868281794460056 0.413896208832524 chr3 198022430 9231939 0.04662067322373531 0.236807117825107 chr4 191154276 7646066 0.039999450496205485 0.2311166578310059 chr5 180915260 5742222 0.03173984328353507 0.20330228220099986 chr6 171115067 7015855 0.041000802109378245 0.22972215697873047 chr7 159138663 6451613 0.04054082696421799 0.347295349327979 chr8 146364022 7725855 0.05278520564295507 0.661049041253252 chr9 141213431 8074079 0.05717642396210881 0.389772723836454 chr10 135534747 5109776 0.03770085615019446 0.3466731153211691 chr11 135006516 4465802 0.03307841822982825 0.27956154990065013 chr12 133851895 4857208 0.036287928534743566 0.21184633271942088 chr13 115169878 4408136 0.038275077446899786 0.21212927095594428 chr14 107349540 2405460 0.0224077345836787 0.17929736631325813 chr15 102531392 2147309 0.020942942040619132 0.15697470995812587 chr16 90354753 2703537 0.02992135897931125 0.2247988633338891 chr17 81195210 2945676 0.03627893812947833 0.21830096390980305 chr18 78077248 3900526 0.04995726796108387 0.6872706597898784 chr19 59128983 2718509 0.04597591336891419 0.48722179438609164 chr20 63025520 2409917 0.038237161708463495 0.2245346304853867 chr21 48129895 1418668 0.029475817472695506 0.20246895158809594 chr22 51304566 1159930 0.022608708940253 0.1620448452276023 chrMT 16571 32767 1.9773701043992518 1.7020972213101053 chrX 155270560 7248645 0.0466839624974625 0.25863208127816445 chrY 59373566 285180 0.004803147582545404 0.11540289059402785