BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708635.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,305,716 number of mapped reads = 2,330,864 (70.51%) number of supplementary alignments = 793 (0.02%) number of secondary alignments = 0 number of mapped bases = 113,295,885 bp number of sequenced bases = 113,273,488 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,349 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9031 >>>>>>> ACTG content number of A's = 33,373,415 bp (29.46%) number of C's = 21,305,021 bp (18.81%) number of T's = 35,737,155 bp (31.55%) number of G's = 22,848,129 bp (20.17%) number of N's = 9,768 bp (0.01%) GC percentage = 38.98% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 732,740 number of insertions = 5,483 mapped reads with insertion percentage = 0.23% number of deletions = 14,826 mapped reads with deletion percentage = 0.63% homopolymer indels = 47.75% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.3505X There is a 3.23% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 8885468 0.035648729637467985 0.6218657266973193 chr2 243199373 9779603 0.04021228706046047 0.37985800555498384 chr3 198022430 7983488 0.04031607934515297 0.2247094011271259 chr4 191154276 7782042 0.040710792156174416 0.22799511027474129 chr5 180915260 7163375 0.039595195010083725 0.22540725970199382 chr6 171115067 6642759 0.038820421348401773 0.2882166870369621 chr7 159138663 6492521 0.0407978858035272 0.5257612954390195 chr8 146364022 6111812 0.0417576117169013 0.5178888548121982 chr9 141213431 4777041 0.03382851734549244 0.29899335493176743 chr10 135534747 5243645 0.03868856596603969 0.28663611290241947 chr11 135006516 5216983 0.03864245337610223 0.29589474500846413 chr12 133851895 5132557 0.03834504546984561 0.2269387787662702 chr13 115169878 3877674 0.03366916825248352 0.2042738955436097 chr14 107349540 3360676 0.03130591896341615 0.20976555165292535 chr15 102531392 3167611 0.030894060230841302 0.1941819812801879 chr16 90354753 2909572 0.032201648539728726 0.21435821896400822 chr17 81195210 2687857 0.03310363998073285 0.2309562646006773 chr18 78077248 3143087 0.04025611917059372 0.6030768852262843 chr19 59128983 1851424 0.03131161582806185 0.46848411447733745 chr20 63025520 2203347 0.03495960049199118 0.21324552930363605 chr21 48129895 1523630 0.03165662422492299 0.21532193059323598 chr22 51304566 1105062 0.021539252471212796 0.16066781537865898 chrMT 16571 3926 0.2369199203427675 0.52857815894959 chrX 155270560 5977841 0.038499513365572974 0.24793117568641565 chrY 59373566 272884 0.00459605205454562 0.09202798082688853