BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081218.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 = 3,182,951 number of mapped reads = 2,823,935 (88.72%) number of supplementary alignments = 30,464 (0.96%) number of secondary alignments = 0 number of mapped bases = 183,455,064 bp number of sequenced bases = 183,386,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,198 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1937 >>>>>>> ACTG content number of A's = 52,038,781 bp (28.38%) number of C's = 35,090,046 bp (19.13%) number of T's = 56,490,168 bp (30.8%) number of G's = 39,755,293 bp (21.68%) number of N's = 12,298 bp (0.01%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,641,536 number of insertions = 13,706 mapped reads with insertion percentage = 0.48% number of deletions = 41,990 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.82% >>>>>>> Coverage mean coverageData = 0.0593X std coverageData = 0.4527X There is a 4.75% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% 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 19076716 0.0765362827320699 0.8410427205976749 chr2 243199373 10821868 0.04449792722121862 0.4855225008207625 chr3 198022430 11847282 0.059827980092962196 0.2957677821681173 chr4 191154276 8548094 0.04471829863748379 0.2622395497651242 chr5 180915260 10588626 0.058528097629796404 0.2904621020953627 chr6 171115067 11520131 0.06732388445957246 0.37969868520069366 chr7 159138663 11961867 0.07516631580598361 0.6669962099435179 chr8 146364022 11405161 0.07792325493761028 0.5346932718859394 chr9 141213431 5919767 0.04192070795305582 0.3592245027184411 chr10 135534747 6596672 0.04867144511657959 0.4223115079277492 chr11 135006516 11179397 0.08280635136158909 0.5030959881015209 chr12 133851895 6348844 0.04743185742719593 0.2686211519493522 chr13 115169878 5153075 0.04474325309261854 0.2534760728606318 chr14 107349540 6137910 0.05717686354315072 0.3023140041344524 chr15 102531392 3714685 0.036229733426422224 0.23302703992786078 chr16 90354753 6051178 0.06697133021878772 0.33537675219443 chr17 81195210 3501957 0.043130093511673906 0.29883581911949675 chr18 78077248 4706797 0.060283848631550126 0.5650023201992704 chr19 59128983 4192201 0.0708992576449353 0.6530239134771293 chr20 63025520 4881760 0.07745687778537964 0.34250490536088285 chr21 48129895 2973101 0.061772438938418626 0.3118633212931989 chr22 51304566 1482904 0.02890393810172763 0.19928080307630983 chrMT 16571 46652 2.8152797055096253 2.653892757463178 chrX 155270560 14296172 0.09207265047540242 0.39941832472361266 chrY 59373566 502247 0.008459101142754336 0.14070484413509138