BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618613.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 35,278,780 number of mapped reads = 33,237,447 (94.21%) number of supplementary alignments = 63,753 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,763,503 number of mapped paired reads (second in pair) = 16,473,944 number of mapped paired reads (both in pair) = 32,626,106 number of mapped paired reads (singletons) = 611,341 number of mapped bases = 3,173,244,150 bp number of sequenced bases = 3,171,071,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,877,000 duplication rate = 20.87% >>>>>>> Insert size mean insert size = 38,611.3063 std insert size = 1,961,234.8006 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 52.5219 >>>>>>> ACTG content number of A's = 855,454,182 bp (26.98%) number of C's = 705,887,860 bp (22.26%) number of T's = 861,683,550 bp (27.17%) number of G's = 747,791,306 bp (23.58%) number of N's = 254,324 bp (0.01%) GC percentage = 45.84% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 35,645,763 number of insertions = 554,572 mapped reads with insertion percentage = 1.64% number of deletions = 1,579,559 mapped reads with deletion percentage = 4.63% homopolymer indels = 53.3% >>>>>>> Coverage mean coverageData = 1.0251X std coverageData = 4.6485X There is a 20.3% of reference with a coverageData >= 1X There is a 13.5% of reference with a coverageData >= 2X There is a 9.86% of reference with a coverageData >= 3X There is a 7.64% of reference with a coverageData >= 4X There is a 6.11% of reference with a coverageData >= 5X There is a 5.01% of reference with a coverageData >= 6X There is a 4.18% of reference with a coverageData >= 7X There is a 3.54% of reference with a coverageData >= 8X There is a 3.04% of reference with a coverageData >= 9X There is a 2.63% of reference with a coverageData >= 10X There is a 2.29% of reference with a coverageData >= 11X There is a 2.01% of reference with a coverageData >= 12X There is a 1.78% of reference with a coverageData >= 13X There is a 1.58% of reference with a coverageData >= 14X There is a 1.42% of reference with a coverageData >= 15X There is a 1.27% of reference with a coverageData >= 16X There is a 1.14% of reference with a coverageData >= 17X There is a 1.03% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.85% of reference with a coverageData >= 20X There is a 0.78% of reference with a coverageData >= 21X There is a 0.71% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.6% of reference with a coverageData >= 24X There is a 0.55% of reference with a coverageData >= 25X There is a 0.51% of reference with a coverageData >= 26X There is a 0.47% of reference with a coverageData >= 27X There is a 0.44% of reference with a coverageData >= 28X There is a 0.4% of reference with a coverageData >= 29X There is a 0.38% of reference with a coverageData >= 30X There is a 0.35% of reference with a coverageData >= 31X There is a 0.33% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.26% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.23% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 292309911 1.1727549958641827 4.973951524617325 chr2 243199373 292146407 1.2012629942101043 5.518777241577242 chr3 198022430 218368251 1.1027450324693016 4.099639508205965 chr4 191154276 156197711 0.8171290450232983 3.5702700640176506 chr5 180915260 183622724 1.014965371080361 3.8337830134153754 chr6 171115067 164299971 0.9601724376498068 3.741929174268866 chr7 159138663 162283971 1.0197645747469928 4.026550609983125 chr8 146364022 156647120 1.0702570061924097 3.9291161602828977 chr9 141213431 143505383 1.0162304108311058 4.482511673322332 chr10 135534747 183472862 1.3536961263520122 5.520810764574379 chr11 135006516 159347717 1.180296490281995 5.593460267347574 chr12 133851895 146309872 1.0930728474184097 4.297824223027315 chr13 115169878 87467660 0.7594664639655171 3.178868423453333 chr14 107349540 109518798 1.0202074270648946 4.325108241465818 chr15 102531392 102183690 0.9966088239590076 4.2997093045450105 chr16 90354753 117748849 1.3031837849194274 8.8817712352419 chr17 81195210 108853320 1.3406372124661048 5.222120801660008 chr18 78077248 81709915 1.0465265758342301 4.342570332971456 chr19 59128983 73577676 1.2443588958734502 5.460573781137997 chr20 63025520 90633407 1.4380429863966215 5.061914443018128 chr21 48129895 43044877 0.8943480346258806 5.854791198301755 chr22 51304566 66583247 1.2978035327304007 5.816803817942648 chrMT 16571 144757 8.735562126606723 37.245976090294405 chrX 155270560 4617555 0.02973876696264894 0.9329731079081077 chrY 59373566 28648499 0.4825126892327808 3.9728284143808543