BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081237.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 = 2,420,814 number of mapped reads = 2,109,111 (87.12%) number of supplementary alignments = 28,851 (1.19%) number of secondary alignments = 0 number of mapped bases = 134,850,229 bp number of sequenced bases = 134,801,358 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,920 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0597 >>>>>>> ACTG content number of A's = 38,982,285 bp (28.92%) number of C's = 26,190,492 bp (19.43%) number of T's = 41,021,598 bp (30.43%) number of G's = 28,598,335 bp (21.22%) number of N's = 8,648 bp (0.01%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,196,957 number of insertions = 9,726 mapped reads with insertion percentage = 0.46% number of deletions = 30,023 mapped reads with deletion percentage = 1.41% homopolymer indels = 47.98% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.3198X There is a 3.46% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14487962 0.05812608186039384 0.5277571387808435 chr2 243199373 10906461 0.04484576117718856 0.3505557690754317 chr3 198022430 10265616 0.05184067279651098 0.27759582870268296 chr4 191154276 4428077 0.023164938251237447 0.18896617844352503 chr5 180915260 7993280 0.04418245315514015 0.2550309984823293 chr6 171115067 9830274 0.057448325108624125 0.3268493133146135 chr7 159138663 8824111 0.0554491965286902 0.40848501960949174 chr8 146364022 7324114 0.05004039858921067 0.40038004346190303 chr9 141213431 2876122 0.020367198641324705 0.2000862708996513 chr10 135534747 3436689 0.025356516141207687 0.2880635442989198 chr11 135006516 7916580 0.05863850304825287 0.34614576243393397 chr12 133851895 4310921 0.032206648998133344 0.21831814654510992 chr13 115169878 3603583 0.03128928381777048 0.2149799836107513 chr14 107349540 5357774 0.049909613026753535 0.27452815767713806 chr15 102531392 2788248 0.027194090957040746 0.20647417324543194 chr16 90354753 4996304 0.055296526570107495 0.2917911828022916 chr17 81195210 1764839 0.021735752638610085 0.19261644377023412 chr18 78077248 3773277 0.04832748459576854 0.37039657699446094 chr19 59128983 3805698 0.06436264936266535 0.4186963409457588 chr20 63025520 3313620 0.05257584546704255 0.2803888665149512 chr21 48129895 2201197 0.04573450658888826 0.26509297297280826 chr22 51304566 920320 0.017938364394311415 0.15948700907803426 chrMT 16571 39720 2.3969585420312596 2.5724544101637066 chrX 155270560 9319988 0.06002417972859762 0.3089916909300297 chrY 59373566 365454 0.006155163393756743 0.10907207258765564