BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505975.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 = 5,130,603 number of mapped reads = 3,602,017 (70.21%) number of supplementary alignments = 213 (0%) number of secondary alignments = 0 number of mapped bases = 168,674,850 bp number of sequenced bases = 168,641,561 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 271,700 duplication rate = 5.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6896 >>>>>>> ACTG content number of A's = 50,115,276 bp (29.72%) number of C's = 34,539,051 bp (20.48%) number of T's = 49,180,527 bp (29.16%) number of G's = 34,806,079 bp (20.64%) number of N's = 628 bp (0%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 846,943 number of insertions = 7,816 mapped reads with insertion percentage = 0.22% number of deletions = 24,253 mapped reads with deletion percentage = 0.67% homopolymer indels = 46.08% >>>>>>> Coverage mean coverageData = 0.0545X std coverageData = 0.5256X There is a 4.14% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13495241 0.05414325928600194 0.7931620431210658 chr2 243199373 14408994 0.05924766097156015 0.4064948615451965 chr3 198022430 11513662 0.05814322145223649 0.30504247478202673 chr4 191154276 10897914 0.05701109192032931 0.3078018395326946 chr5 180915260 10424340 0.05762001502803025 0.305426803154602 chr6 171115067 10203190 0.0596276539458679 0.3947621511520653 chr7 159138663 9951921 0.06253616068145552 0.8046749072471141 chr8 146364022 8651956 0.05911258710832639 0.72231680535242 chr9 141213431 7140636 0.05056626660391815 0.3727589490304709 chr10 135534747 7395526 0.054565535139118236 0.49946709556500857 chr11 135006516 7736743 0.0573064414165017 0.41971594070896306 chr12 133851895 7552175 0.05642187583522818 0.3230771554154163 chr13 115169878 5509036 0.047834000484050176 0.2751480134943449 chr14 107349540 5819544 0.054211168487540796 1.278536546323414 chr15 102531392 4584581 0.04471392527275939 0.2641994846575246 chr16 90354753 4540202 0.05024862388810913 0.30735265244926285 chr17 81195210 4159325 0.05122623612895391 0.3249330316500594 chr18 78077248 4172252 0.05343748796064124 0.7163757270599573 chr19 59128983 2986253 0.0505040480740215 0.6529314928212718 chr20 63025520 3155243 0.05006294275715615 0.29922727318462394 chr21 48129895 2077579 0.0431660821200628 0.28024053900691653 chr22 51304566 1874629 0.036539223428963416 0.23985574713238897 chrMT 16571 27151 1.6384647878824452 1.8210199506979572 chrX 155270560 9936091 0.06399211157607727 0.35870956864657894 chrY 59373566 460666 0.00775877264976808 0.13256311961394754