BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695926.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 13,129,814 number of mapped reads = 12,096,889 (92.13%) number of supplementary alignments = 297,558 (2.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,092,983 number of mapped paired reads (second in pair) = 6,003,906 number of mapped paired reads (both in pair) = 11,495,058 number of mapped paired reads (singletons) = 601,831 number of mapped bases = 1,018,575,617 bp number of sequenced bases = 1,018,180,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,799,076 duplication rate = 14.5% >>>>>>> Insert size mean insert size = 278,253.4171 std insert size = 5,087,635.7786 median insert size = 296 >>>>>>> Mapping quality mean mapping quality = 51.3876 >>>>>>> ACTG content number of A's = 275,246,700 bp (27.03%) number of C's = 181,458,199 bp (17.82%) number of T's = 330,088,130 bp (32.42%) number of G's = 231,054,433 bp (22.69%) number of N's = 332,976 bp (0.03%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 12,711,754 number of insertions = 83,785 mapped reads with insertion percentage = 0.68% number of deletions = 219,155 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.329X std coverageData = 2.8998X There is a 16.21% of reference with a coverageData >= 1X There is a 6.93% of reference with a coverageData >= 2X There is a 3.44% of reference with a coverageData >= 3X There is a 1.89% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.7% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 78959072 0.31678585867996695 6.279690284468998 chr2 243199373 85043710 0.34968720910312545 3.1602133296492223 chr3 198022430 67718460 0.3419736844962462 1.0635136813615012 chr4 191154276 68794875 0.35989189695134 1.2786665177777443 chr5 180915260 74461665 0.41158310802527104 1.258337157196288 chr6 171115067 59974612 0.3504928762351477 1.6868089379635258 chr7 159138663 66456233 0.41759954336175364 3.4074099919938856 chr8 146364022 59633453 0.40743245631771446 4.29415776737977 chr9 141213431 40375275 0.2859166774299252 2.606470434277719 chr10 135534747 46288877 0.3415277486001431 3.341738891049392 chr11 135006516 48197812 0.3570035982559538 2.2412883786956184 chr12 133851895 47891297 0.35779319373849733 1.145840326075493 chr13 115169878 34856620 0.3026539630440522 1.0169195058761158 chr14 107349540 30587328 0.2849320826153517 1.2357836663620005 chr15 102531392 32014528 0.3122412304711517 1.0377208869091508 chr16 90354753 27159009 0.3005819627441182 1.2831288365392464 chr17 81195210 25435314 0.31326126257940584 1.7573347942666864 chr18 78077248 28228274 0.36154289147076496 4.525434486753162 chr19 59128983 15957395 0.2698743355690728 4.379523410209194 chr20 63025520 17265849 0.2739501236959251 1.048801005850798 chr21 48129895 13155920 0.27334196345119804 2.266687595329343 chr22 51304566 9567875 0.1864916857497635 1.6264719115362385 chrMT 16571 1746080 105.36962162814555 69.49516400233992 chrX 155270560 29195016 0.18802673217640228 1.0987472056598058 chrY 59373566 9611068 0.1618745284728224 1.5866289231979847