BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082909.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 = 1,660,616 number of mapped reads = 1,458,334 (87.82%) number of supplementary alignments = 19,469 (1.17%) number of secondary alignments = 0 number of mapped bases = 95,927,044 bp number of sequenced bases = 95,891,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,491 duplication rate = 5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9222 >>>>>>> ACTG content number of A's = 26,081,427 bp (27.2%) number of C's = 17,729,953 bp (18.49%) number of T's = 30,486,573 bp (31.79%) number of G's = 21,589,053 bp (22.51%) number of N's = 4,224 bp (0%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 711,020 number of insertions = 7,827 mapped reads with insertion percentage = 0.53% number of deletions = 22,084 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.031X std coverageData = 0.2789X There is a 2.49% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.1% 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% 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 8954251 0.03592468882956163 0.3992806912969169 chr2 243199373 11117675 0.045714242034661824 0.47431396823640215 chr3 198022430 5982813 0.030212804680762678 0.2094133434804474 chr4 191154276 5277032 0.02760614154401652 0.20236498333503325 chr5 180915260 4841673 0.026762103981720502 0.19861130209640127 chr6 171115067 6399928 0.03740131194876019 0.2819846071193601 chr7 159138663 4704363 0.02956140834235864 0.23902289606350358 chr8 146364022 6166612 0.04213202066830331 0.29701540280737 chr9 141213431 2659097 0.018830340578581368 0.22793658865314578 chr10 135534747 3865421 0.0285197787693513 0.21826151395612411 chr11 135006516 3848137 0.028503342757174772 0.23375864384482636 chr12 133851895 2874135 0.021472501379229632 0.18010728425670344 chr13 115169878 2202494 0.0191238719554778 0.16714706474340352 chr14 107349540 1879386 0.017507163980395257 0.16687669589513723 chr15 102531392 3154471 0.030765904358345197 0.21330358988472256 chr16 90354753 3498739 0.03872224629953889 0.2451259233707263 chr17 81195210 2441096 0.030064532131883148 0.21473299985388147 chr18 78077248 3913455 0.050122860375406676 0.4712966850388743 chr19 59128983 2215805 0.03747409286576094 0.3324639703347352 chr20 63025520 1844690 0.029268937408211786 0.21848625110680026 chr21 48129895 2993858 0.06220370935777026 0.3067175192466576 chr22 51304566 1493562 0.029111677896271455 0.20511829287578917 chrMT 16571 143256 8.64498219781546 6.155485206414574 chrX 155270560 3290873 0.02119444278425994 0.18895216137433812 chrY 59373566 164222 0.002765911011644475 0.06632938686927535