BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506340.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 = 5,475,824 number of mapped reads = 3,567,876 (65.16%) number of supplementary alignments = 49,949 (0.91%) number of secondary alignments = 0 number of mapped bases = 273,563,984 bp number of sequenced bases = 273,449,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 476,484 duplication rate = 10.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2404 >>>>>>> ACTG content number of A's = 76,820,653 bp (28.09%) number of C's = 49,364,365 bp (18.05%) number of T's = 78,097,919 bp (28.56%) number of G's = 69,103,133 bp (25.27%) number of N's = 63,721 bp (0.02%) GC percentage = 43.32% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,201,223 number of insertions = 22,895 mapped reads with insertion percentage = 0.63% number of deletions = 57,267 mapped reads with deletion percentage = 1.58% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.0884X std coverageData = 0.6084X There is a 5.87% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 20607457 0.08267765559548997 0.8408824744841549 chr2 243199373 21648385 0.08901497044566804 0.6407211142079247 chr3 198022430 17445586 0.0880990400935894 0.4249630408250474 chr4 191154276 17409150 0.09107381934788632 0.6480207148200192 chr5 180915260 20718276 0.11451922850510234 0.48944506626637857 chr6 171115067 10645135 0.06221038969058172 0.38381075545951354 chr7 159138663 13913041 0.08742715778628855 0.7036904514851053 chr8 146364022 16319713 0.11150085093999398 0.8636929181860512 chr9 141213431 7656348 0.05421827049864683 0.5129274122434043 chr10 135534747 15872312 0.11710880310272022 0.743093131028963 chr11 135006516 12103694 0.08965266535727802 0.6110023979397378 chr12 133851895 11867609 0.08866224120323436 0.45907383092626997 chr13 115169878 5496085 0.0477215492057741 0.3071950950066522 chr14 107349540 7715665 0.07187422507818851 0.42296684882138985 chr15 102531392 9933210 0.09687969514741397 0.46500268099152 chr16 90354753 9957929 0.11020924377935049 0.5786353982618039 chr17 81195210 7167675 0.08827706708314444 0.48076437325101073 chr18 78077248 4957945 0.06350050913679745 0.8969534495404597 chr19 59128983 6836936 0.11562749185116206 0.7154386385223211 chr20 63025520 7049441 0.11185058052674536 0.5329385418348875 chr21 48129895 4489408 0.09327691240548104 0.5751429077156479 chr22 51304566 3299287 0.06430786296876578 0.38671945598603963 chrMT 16571 13525 0.8161849013336552 1.6622695942303163 chrX 155270560 19428639 0.12512764171134566 0.5527466858212629 chrY 59373566 1011533 0.017036756727733013 0.604689842191747