BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084267.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 = 1,731,971 number of mapped reads = 1,417,778 (81.86%) number of supplementary alignments = 8,676 (0.5%) number of secondary alignments = 0 number of mapped bases = 92,197,170 bp number of sequenced bases = 92,164,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,613 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2714 >>>>>>> ACTG content number of A's = 27,085,096 bp (29.39%) number of C's = 17,293,637 bp (18.76%) number of T's = 27,599,877 bp (29.95%) number of G's = 20,185,042 bp (21.9%) number of N's = 1,032 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 801,703 number of insertions = 6,989 mapped reads with insertion percentage = 0.49% number of deletions = 20,328 mapped reads with deletion percentage = 1.42% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 0.2493X There is a 2.7% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% 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 7171863 0.0287737016310182 0.35333671429311475 chr2 243199373 7860621 0.03232171573073916 0.29880048979166174 chr3 198022430 6191768 0.03126801342655981 0.1902647584885825 chr4 191154276 6161983 0.03223565346767341 0.19751990094658944 chr5 180915260 5366336 0.029662152324795597 0.18533204104427276 chr6 171115067 5495347 0.03211492182625859 0.22030194010975532 chr7 159138663 5160846 0.03242986903817333 0.320828107097872 chr8 146364022 4691236 0.03205183853173972 0.26685113264685534 chr9 141213431 3940806 0.027906736435006668 0.24002391794338368 chr10 135534747 4288135 0.03163863949958161 0.2532304038132791 chr11 135006516 4172716 0.030907515604654223 0.23279022177533565 chr12 133851895 4242578 0.031696062278386124 0.19302509119984113 chr13 115169878 3011584 0.026149059565731242 0.1736608985080989 chr14 107349540 2784608 0.025939636071100072 0.18582870379668126 chr15 102531392 2664948 0.025991532427454025 0.17674220960875947 chr16 90354753 2619479 0.028991048207502708 0.20389663623660317 chr17 81195210 2412238 0.0297091170772266 0.21010670649700924 chr18 78077248 2478036 0.031738260037034095 0.49306864391851474 chr19 59128983 1763997 0.029833034672691734 0.2867513112243331 chr20 63025520 1873881 0.02973209899735853 0.1941578292727445 chr21 48129895 1209621 0.025132425491474684 0.1773530965373068 chr22 51304566 990833 0.019312764481820194 0.14862678634953197 chrMT 16571 26729 1.6129986120330697 1.777754302881192 chrX 155270560 5393926 0.03473888417739976 0.21712023211791603 chrY 59373566 223055 0.003756806522282997 0.08308139453063133