BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081008.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 = 3,525,209 number of mapped reads = 2,941,949 (83.45%) number of supplementary alignments = 15,898 (0.45%) number of secondary alignments = 0 number of mapped bases = 187,259,330 bp number of sequenced bases = 187,192,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,810 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7076 >>>>>>> ACTG content number of A's = 52,791,620 bp (28.2%) number of C's = 37,766,582 bp (20.18%) number of T's = 55,008,276 bp (29.39%) number of G's = 41,623,096 bp (22.24%) number of N's = 2,432 bp (0%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,437,086 number of insertions = 13,025 mapped reads with insertion percentage = 0.44% number of deletions = 38,803 mapped reads with deletion percentage = 1.31% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 0.0605X std coverageData = 0.4504X There is a 4.94% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 16176347 0.06489992656828726 0.7503674538504694 chr2 243199373 15272776 0.06279940532576948 0.4580800697177809 chr3 198022430 12610327 0.06368130620354472 0.2955049527062332 chr4 191154276 11803605 0.0617491025939697 0.3081048279063043 chr5 180915260 11284839 0.06237637996927401 0.2957067508577874 chr6 171115067 11064557 0.06466150055623097 0.4393630094665806 chr7 159138663 10416670 0.06545656350022244 0.7484976561720219 chr8 146364022 9300788 0.06354558909292612 0.4402385929433377 chr9 141213431 8205658 0.058108197937631015 0.4330946941337311 chr10 135534747 9753340 0.07196191541937212 0.40287167967589477 chr11 135006516 8277944 0.06131514422607572 0.41828781321813696 chr12 133851895 7743288 0.0578496703389967 0.29297957098272653 chr13 115169878 5431564 0.04716132459565513 0.2558193548020997 chr14 107349540 5993619 0.05583274041043865 0.3032095839049926 chr15 102531392 5469729 0.05334687156105322 0.2844677030086914 chr16 90354753 5403141 0.05979918953461142 0.32319570447661533 chr17 81195210 5171690 0.06369452089599867 0.35732819216701905 chr18 78077248 4247269 0.05439829282917349 0.8022757073971045 chr19 59128983 3569410 0.060366504189662794 0.5797931827972864 chr20 63025520 4178235 0.06629433600865173 0.3153502439689426 chr21 48129895 2580975 0.05362519490225358 0.29930597018389754 chr22 51304566 2069854 0.040344440297964905 0.23764498023785388 chrMT 16571 59453 3.587773821736769 3.5791395640790338 chrX 155270560 10703678 0.06893565657263039 0.35970160766248144 chrY 59373566 470574 0.007925648259024901 0.15575925408338287