BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618586.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 = 66,580,650 number of mapped reads = 61,360,840 (92.16%) number of supplementary alignments = 244,903 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,007,564 number of mapped paired reads (second in pair) = 30,353,276 number of mapped paired reads (both in pair) = 60,037,472 number of mapped paired reads (singletons) = 1,323,368 number of mapped bases = 5,714,809,731 bp number of sequenced bases = 5,710,829,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,524,529 duplication rate = 20.13% >>>>>>> Insert size mean insert size = 71,113.239 std insert size = 2,655,411.3912 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 51.9617 >>>>>>> ACTG content number of A's = 1,562,650,884 bp (27.36%) number of C's = 1,225,734,439 bp (21.46%) number of T's = 1,587,882,090 bp (27.8%) number of G's = 1,334,344,203 bp (23.37%) number of N's = 217,649 bp (0%) GC percentage = 44.83% >>>>>>> Mismatches and indels general error rate = 0.0135 number of mismatches = 75,627,192 number of insertions = 1,043,532 mapped reads with insertion percentage = 1.68% number of deletions = 2,938,630 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.69% >>>>>>> Coverage mean coverageData = 1.8461X std coverageData = 6.7795X There is a 29.19% of reference with a coverageData >= 1X There is a 20.86% of reference with a coverageData >= 2X There is a 16.1% of reference with a coverageData >= 3X There is a 13.03% of reference with a coverageData >= 4X There is a 10.81% of reference with a coverageData >= 5X There is a 9.15% of reference with a coverageData >= 6X There is a 7.86% of reference with a coverageData >= 7X There is a 6.82% of reference with a coverageData >= 8X There is a 5.97% of reference with a coverageData >= 9X There is a 5.27% of reference with a coverageData >= 10X There is a 4.68% of reference with a coverageData >= 11X There is a 4.18% of reference with a coverageData >= 12X There is a 3.75% of reference with a coverageData >= 13X There is a 3.38% of reference with a coverageData >= 14X There is a 3.06% of reference with a coverageData >= 15X There is a 2.77% of reference with a coverageData >= 16X There is a 2.53% of reference with a coverageData >= 17X There is a 2.3% of reference with a coverageData >= 18X There is a 2.11% of reference with a coverageData >= 19X There is a 1.93% of reference with a coverageData >= 20X There is a 1.78% of reference with a coverageData >= 21X There is a 1.63% of reference with a coverageData >= 22X There is a 1.51% of reference with a coverageData >= 23X There is a 1.39% of reference with a coverageData >= 24X There is a 1.29% of reference with a coverageData >= 25X There is a 1.19% of reference with a coverageData >= 26X There is a 1.11% of reference with a coverageData >= 27X There is a 1.03% of reference with a coverageData >= 28X There is a 0.96% of reference with a coverageData >= 29X There is a 0.89% of reference with a coverageData >= 30X There is a 0.83% of reference with a coverageData >= 31X There is a 0.78% of reference with a coverageData >= 32X There is a 0.73% of reference with a coverageData >= 33X There is a 0.68% of reference with a coverageData >= 34X There is a 0.64% of reference with a coverageData >= 35X There is a 0.6% of reference with a coverageData >= 36X There is a 0.56% of reference with a coverageData >= 37X There is a 0.52% of reference with a coverageData >= 38X There is a 0.49% of reference with a coverageData >= 39X There is a 0.46% of reference with a coverageData >= 40X There is a 0.44% of reference with a coverageData >= 41X There is a 0.41% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.36% of reference with a coverageData >= 44X There is a 0.34% of reference with a coverageData >= 45X There is a 0.32% of reference with a coverageData >= 46X There is a 0.31% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 516139050 2.070763346262636 8.5512938166134 chr2 243199373 505948618 2.0803861940877617 7.377766004969658 chr3 198022430 392412906 1.981658875714231 5.8601871326793225 chr4 191154276 319341456 1.670595409542395 5.87480911694336 chr5 180915260 344862825 1.9062119193262084 5.734746292041216 chr6 171115067 324593634 1.8969319282678947 6.0819699941888645 chr7 159138663 303540031 1.907393371779176 6.07119959635308 chr8 146364022 292751328 2.000159082810665 6.282750967667429 chr9 141213431 257021969 1.8200957740344117 8.255082441502728 chr10 135534747 298026364 2.1988926869063325 6.771495508690459 chr11 135006516 294563932 2.181849741237675 7.7011661636106155 chr12 133851895 271518265 2.028497728777019 6.304012654606277 chr13 115169878 161477496 1.4020809850992462 4.755773912556248 chr14 107349540 185467170 1.727694128917553 5.883946689152492 chr15 102531392 189719830 1.850358473627277 6.125645080969046 chr16 90354753 209106097 2.3142788846979636 9.235722163331967 chr17 81195210 182779806 2.251115626155779 7.424801931503048 chr18 78077248 151572182 1.9413105082802098 8.441703654150022 chr19 59128983 115915078 1.960376656571279 7.392632855194624 chr20 63025520 161022433 2.5548767070862723 7.625129894645128 chr21 48129895 73611709 1.5294383875136233 9.317008317152238 chr22 51304566 97853465 1.9073051899513194 7.260117066863567 chrMT 16571 748 0.045139098424959265 0.3556687627633781 chrX 155270560 11338681 0.0730253114305764 1.8049327809829598 chrY 59373566 54224658 0.9132794550355962 4.893685554714004