BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548987.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,944,288 number of mapped reads = 3,421,877 (43.07%) number of secondary alignments = 0 number of mapped bases = 134,762,168 bp number of sequenced bases = 134,744,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,038 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5225 >>>>>>> ACTG content number of A's = 40,174,164 bp (29.82%) number of C's = 26,964,699 bp (20.01%) number of T's = 40,605,159 bp (30.14%) number of G's = 26,992,934 bp (20.03%) number of N's = 7,213 bp (0.01%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 442,006 number of insertions = 6,598 mapped reads with insertion percentage = 0.19% number of deletions = 14,485 mapped reads with deletion percentage = 0.42% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.0435X std coverageData = 0.3589X There is a 3.57% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 10687491 0.042878492968729656 0.5690942400238211 chr2 243199373 11815356 0.048583003542529694 0.32625631502219404 chr3 198022430 9519300 0.04807182701474778 0.25913145356163775 chr4 191154276 9077916 0.04748999703255396 0.26524776145897005 chr5 180915260 8496085 0.046961682502625814 0.2576512994181609 chr6 171115067 7964643 0.04654553885661045 0.2857719902065536 chr7 159138663 7776167 0.04886409658977718 0.47077524042648683 chr8 146364022 7145081 0.048817194979788134 0.7537493111566794 chr9 141213431 5710682 0.04044007683660062 0.2789441992140747 chr10 135534747 6449572 0.047586114577688333 0.2927974772594147 chr11 135006516 6215530 0.046038740826405744 0.30537031822283467 chr12 133851895 6120260 0.04572411918411764 0.2588887402372422 chr13 115169878 4584781 0.0398088552286215 0.23712883270138702 chr14 107349540 4235730 0.039457365164303454 0.25373085259550404 chr15 102531392 3802699 0.03708814369749316 0.22705349623791346 chr16 90354753 3758175 0.041593550701201076 0.24817077355860367 chr17 81195210 3533840 0.043522764458642324 0.25653912145406993 chr18 78077248 3652838 0.0467849225423519 0.4233559086314823 chr19 59128983 2565318 0.043385119612153654 0.4728360134939549 chr20 63025520 2823931 0.04480615153988416 0.25407898745661583 chr21 48129895 1762490 0.03661944411056787 0.239763606356593 chr22 51304566 1521162 0.029649641710252455 0.23629866514401085 chrMT 16571 6428 0.3879065837909601 0.676524836467642 chrX 155270560 4462144 0.028737862476956352 0.22467987743661966 chrY 59373566 1074549 0.018098104466219865 0.2034508212238086