BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506123.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 = 6,104,835 number of mapped reads = 4,821,846 (78.98%) number of supplementary alignments = 75,861 (1.24%) number of secondary alignments = 0 number of mapped bases = 389,515,524 bp number of sequenced bases = 389,337,704 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 888,567 duplication rate = 12.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9186 >>>>>>> ACTG content number of A's = 106,163,782 bp (27.27%) number of C's = 72,770,971 bp (18.69%) number of T's = 112,600,879 bp (28.92%) number of G's = 97,734,737 bp (25.1%) number of N's = 67,335 bp (0.02%) GC percentage = 43.79% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 2,989,122 number of insertions = 34,984 mapped reads with insertion percentage = 0.71% number of deletions = 85,805 mapped reads with deletion percentage = 1.74% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.1258X std coverageData = 0.9773X There is a 7.09% of reference with a coverageData >= 1X There is a 2.6% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 26412833 0.10596897570016485 1.7281294259715254 chr2 243199373 30799839 0.12664440134062352 1.058418162127123 chr3 198022430 24167657 0.12204504812914375 0.5703203359108644 chr4 191154276 24073460 0.12593733451194156 0.9763275256160707 chr5 180915260 29384011 0.1624186428496966 0.6720788512626855 chr6 171115067 13685621 0.07997905292583031 0.49656188244649857 chr7 159138663 20605243 0.12947980466569586 1.078984025598367 chr8 146364022 24775180 0.16927097015686 1.0771301468042256 chr9 141213431 9976964 0.07065166485474034 0.8226159720597881 chr10 135534747 23191459 0.17111080009615542 1.286799359423516 chr11 135006516 17248134 0.12775778911293437 0.904218034444975 chr12 133851895 16379128 0.1223675466081373 0.5903903185510285 chr13 115169878 8033305 0.06975178874462297 0.4286690111667337 chr14 107349540 11199250 0.1043250860693022 0.5972022462494988 chr15 102531392 14189882 0.13839548769609994 0.6259238088756952 chr16 90354753 14912418 0.1650429834056433 0.8432077929375147 chr17 81195210 10632095 0.13094485499821973 0.7137548173457253 chr18 78077248 7080970 0.09069184917993012 1.3480518756001472 chr19 59128983 10136078 0.17142317499355603 1.2785144007229745 chr20 63025520 11412862 0.181083186620277 0.7718770653483689 chr21 48129895 6538933 0.13586011355312536 0.8795779103880504 chr22 51304566 4744419 0.09247557030304086 0.5466555495657677 chrMT 16571 13651 0.8237885462555066 2.7157433155182678 chrX 155270560 28129318 0.18116324176328083 0.7853198815550624 chrY 59373566 1792814 0.030195491374056933 1.3220390176597703