BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505977.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 10,541,890 number of mapped reads = 7,843,182 (74.4%) number of supplementary alignments = 297 (0%) number of secondary alignments = 0 number of mapped bases = 366,243,689 bp number of sequenced bases = 366,173,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 489,502 duplication rate = 4.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8675 >>>>>>> ACTG content number of A's = 112,294,123 bp (30.67%) number of C's = 71,430,209 bp (19.51%) number of T's = 109,777,900 bp (29.98%) number of G's = 72,669,706 bp (19.85%) number of N's = 1,683 bp (0%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,698,751 number of insertions = 16,710 mapped reads with insertion percentage = 0.21% number of deletions = 51,507 mapped reads with deletion percentage = 0.66% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.1183X std coverageData = 1.1153X There is a 8.08% of reference with a coverageData >= 1X There is a 2.38% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 28013945 0.11239267885314516 2.470129700156966 chr2 243199373 31466074 0.1293838615282943 0.875086414667623 chr3 198022430 25315996 0.1278440831172509 0.5167977746173914 chr4 191154276 24868408 0.13009600685050854 0.4993394673657732 chr5 180915260 23375839 0.12920877431787678 0.519227348771218 chr6 171115067 21981968 0.12846307683706193 0.638632153233612 chr7 159138663 20070236 0.1261179126533192 1.42117338448004 chr8 146364022 19677073 0.13443927497428296 1.7684225612130116 chr9 141213431 14986514 0.10612668988971737 0.7716423732313652 chr10 135534747 17089551 0.12608981370659142 1.1047708358972017 chr11 135006516 16670402 0.12347849936368997 0.9242147615479785 chr12 133851895 16679194 0.12460932286390118 0.5356776463684497 chr13 115169878 13135646 0.11405452734785393 0.45170016660237794 chr14 107349540 11683382 0.10883495169145578 0.9997959318572299 chr15 102531392 10070832 0.09822193772615513 0.42335410395354384 chr16 90354753 9190313 0.10171366413895239 0.5753527708213603 chr17 81195210 8329355 0.10258431501070076 0.5449802670577362 chr18 78077248 9917024 0.12701554235108287 1.9598525751852869 chr19 59128983 5870413 0.09928148096171382 1.4805114667826964 chr20 63025520 6880705 0.10917331582508165 0.47542780047818123 chr21 48129895 4987249 0.10362060835578386 0.5008326830948702 chr22 51304566 3421131 0.06668277829306654 0.34618487370583767 chrMT 16571 23013 1.3887514332267215 1.5544245362087288 chrX 155270560 21595953 0.1390859477804421 0.6832078831254114 chrY 59373566 943473 0.01589045535853447 0.24409555680096634