BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083623.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,834,719 number of mapped reads = 1,674,775 (91.28%) number of supplementary alignments = 19,893 (1.08%) number of secondary alignments = 0 number of mapped bases = 111,266,991 bp number of sequenced bases = 111,225,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,659 duplication rate = 4.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8566 >>>>>>> ACTG content number of A's = 30,479,217 bp (27.4%) number of C's = 20,228,541 bp (18.19%) number of T's = 35,670,774 bp (32.07%) number of G's = 24,841,344 bp (22.33%) number of N's = 6,034 bp (0.01%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 772,409 number of insertions = 8,273 mapped reads with insertion percentage = 0.49% number of deletions = 25,675 mapped reads with deletion percentage = 1.52% homopolymer indels = 48.11% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.3479X There is a 2.99% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 11636481 0.04668586562919737 0.6967281792805312 chr2 243199373 8756072 0.03600367834829903 0.42831881656130566 chr3 198022430 9507484 0.048012157006658285 0.2595903551407792 chr4 191154276 4975788 0.026030220741700805 0.1959663803247967 chr5 180915260 5591752 0.03090812792685371 0.20443916882151195 chr6 171115067 8906048 0.0520471291987397 0.3388271607280383 chr7 159138663 8729601 0.05485531193635829 0.5701526987225145 chr8 146364022 7396542 0.05053524697483375 0.4035042243562488 chr9 141213431 4328184 0.030649945754805716 0.23329802875705732 chr10 135534747 5434157 0.0400941981320849 0.28436704878524033 chr11 135006516 3485121 0.025814465132927362 0.20829339513234046 chr12 133851895 3901105 0.029144936648076592 0.19907342100697065 chr13 115169878 3598448 0.031244697506756063 0.20829234610449845 chr14 107349540 2616542 0.024374040168220562 0.18299535007782294 chr15 102531392 2340743 0.0228295252248209 0.1806056551173877 chr16 90354753 2565450 0.02839308298479882 0.2007840256974288 chr17 81195210 2326157 0.028648943700003978 0.20059620914142887 chr18 78077248 2896851 0.037102370718804026 0.3508195915128447 chr19 59128983 3009639 0.050899556314033 0.4823455756947145 chr20 63025520 2043555 0.03242424655917159 0.2148982364714707 chr21 48129895 1700250 0.035326276942843945 0.22082932987272955 chr22 51304566 683134 0.013315267105075988 0.13056598744103334 chrMT 16571 3385 0.20427252428942128 0.5946443688192409 chrX 155270560 4611909 0.029702404628411207 0.20734387261050355 chrY 59373566 222593 0.0037490252817221725 0.07972189998000798