BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926912.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 25,946,110 number of mapped reads = 24,946,532 (96.15%) number of supplementary alignments = 955,428 (3.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,554,883 number of mapped paired reads (second in pair) = 12,391,649 number of mapped paired reads (both in pair) = 24,446,766 number of mapped paired reads (singletons) = 499,766 number of mapped bases = 2,223,442,472 bp number of sequenced bases = 2,221,666,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,660,428 duplication rate = 8.71% >>>>>>> Insert size mean insert size = 444,641.8504 std insert size = 6,546,148.4636 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.3014 >>>>>>> ACTG content number of A's = 632,121,804 bp (28.45%) number of C's = 429,042,065 bp (19.31%) number of T's = 644,404,104 bp (29.01%) number of G's = 515,927,746 bp (23.22%) number of N's = 170,466 bp (0.01%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 23,277,631 number of insertions = 381,595 mapped reads with insertion percentage = 1.51% number of deletions = 1,209,294 mapped reads with deletion percentage = 4.72% homopolymer indels = 51.86% >>>>>>> Coverage mean coverageData = 0.7182X std coverageData = 2.1575X There is a 30.56% of reference with a coverageData >= 1X There is a 16.01% of reference with a coverageData >= 2X There is a 8.78% of reference with a coverageData >= 3X There is a 5.27% of reference with a coverageData >= 4X There is a 3.29% of reference with a coverageData >= 5X There is a 2.14% of reference with a coverageData >= 6X There is a 1.43% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.69% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 181922276 0.7298769217509793 2.1221586269776727 chr2 243199373 191507174 0.787449291655863 3.1861450079789204 chr3 198022430 151266050 0.7638834146212629 1.6483216207479297 chr4 191154276 134119039 0.7016271977091425 1.736740021978374 chr5 180915260 135950044 0.751457030214035 1.623230039591056 chr6 171115067 128382035 0.7502672748274118 1.805058522584567 chr7 159138663 114004247 0.7163830891302637 1.7508298298583151 chr8 146364022 113971652 0.7786862539210626 1.7607357589103259 chr9 141213431 95809510 0.678473069604831 2.332548898731919 chr10 135534747 106076375 0.7826507766307337 2.995919218424765 chr11 135006516 106132175 0.7861263155624281 1.9595799670379095 chr12 133851895 101535883 0.758568886902946 1.7975576413616683 chr13 115169878 66956969 0.5813757048522705 1.4345862105022926 chr14 107349540 67857715 0.6321192899382708 1.5509104228091024 chr15 102531392 66748925 0.6510096439537268 1.6443705778569127 chr16 90354753 66271082 0.7334542987461877 2.3874010858791146 chr17 81195210 56373739 0.6942988262484943 1.639258589465716 chr18 78077248 58536369 0.7497237735633305 2.132447964888191 chr19 59128983 36012204 0.6090448739833729 1.6924149555212085 chr20 63025520 51169094 0.8118789658538319 1.801656114411179 chr21 48129895 28151927 0.5849156122198064 2.0363604202165235 chr22 51304566 27835939 0.5425626054413948 1.5232901292223595 chrMT 16571 4280622 258.320077243377 179.7674796194516 chrX 155270560 129309732 0.8328026381820224 1.7771688443147875 chrY 59373566 3261695 0.054935137296621195 1.1363686036064602