BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506087.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 = 6,933,762 number of mapped reads = 5,756,978 (83.03%) number of supplementary alignments = 107,214 (1.55%) number of secondary alignments = 0 number of mapped bases = 455,639,805 bp number of sequenced bases = 455,447,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,311,253 duplication rate = 14.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6026 >>>>>>> ACTG content number of A's = 119,488,345 bp (26.24%) number of C's = 87,203,779 bp (19.15%) number of T's = 136,903,084 bp (30.06%) number of G's = 111,775,102 bp (24.54%) number of N's = 76,743 bp (0.02%) GC percentage = 43.69% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 3,679,917 number of insertions = 39,411 mapped reads with insertion percentage = 0.67% number of deletions = 94,640 mapped reads with deletion percentage = 1.61% homopolymer indels = 42.46% >>>>>>> Coverage mean coverageData = 0.1472X std coverageData = 1.2523X There is a 7.1% of reference with a coverageData >= 1X There is a 3.1% of reference with a coverageData >= 2X There is a 1.6% of reference with a coverageData >= 3X There is a 0.91% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 35531487 0.142553253658694 2.4113700219832523 chr2 243199373 34760987 0.14293205846381848 1.2717071335359544 chr3 198022430 27332995 0.1380297928876037 0.6879575082308045 chr4 191154276 28462752 0.14889937382305798 1.101420591852093 chr5 180915260 35701047 0.1973357416063189 0.8570518601777068 chr6 171115067 15382811 0.08989746648084473 0.6284389776620596 chr7 159138663 22522462 0.14152727926336794 1.2903504196465139 chr8 146364022 31034479 0.21203625437404283 1.3792048926896723 chr9 141213431 12112515 0.08577452522911931 1.0706857406040415 chr10 135534747 28503457 0.21030368692096352 1.50026847184846 chr11 135006516 20921190 0.1549642981676529 1.1801844765815512 chr12 133851895 20193477 0.15086433404622326 0.7924398943393111 chr13 115169878 9896355 0.08592832754411704 0.5403040376078885 chr14 107349540 13145294 0.12245319355816522 0.7674392940440672 chr15 102531392 13596333 0.13260653868817074 0.6967438271415907 chr16 90354753 17282531 0.19127417679953151 1.046340178879325 chr17 81195210 12368570 0.15233127668491775 0.890890047953505 chr18 78077248 7443469 0.0953346741934347 2.118202455928362 chr19 59128983 10815761 0.18291809618981608 1.7265825975526232 chr20 63025520 13001668 0.20629211785955912 0.9672000481907073 chr21 48129895 7371575 0.15316000585498887 1.1937024969704908 chr22 51304566 5854321 0.11410916135612569 0.7285689498353336 chrMT 16571 61657 3.7207772614809005 3.700391157342294 chrX 155270560 30603987 0.19710102803776838 0.9455655134198998 chrY 59373566 1738625 0.02928281248931553 1.0700116271357047