BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038392.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,770,586 number of mapped reads = 18,180,902 (96.86%) number of supplementary alignments = 217,235 (1.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,184,398 number of mapped paired reads (second in pair) = 8,996,504 number of mapped paired reads (both in pair) = 17,955,174 number of mapped paired reads (singletons) = 225,728 number of mapped bases = 2,478,572,518 bp number of sequenced bases = 2,477,045,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,410,143 duplication rate = 14.59% >>>>>>> Insert size mean insert size = 66,448.6068 std insert size = 2,583,309.8463 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 53.6262 >>>>>>> ACTG content number of A's = 685,467,433 bp (27.67%) number of C's = 520,846,771 bp (21.03%) number of T's = 693,088,609 bp (27.98%) number of G's = 577,437,245 bp (23.31%) number of N's = 205,523 bp (0.01%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 28,124,256 number of insertions = 355,332 mapped reads with insertion percentage = 1.87% number of deletions = 811,571 mapped reads with deletion percentage = 4.32% homopolymer indels = 48.17% >>>>>>> Coverage mean coverageData = 0.8007X std coverageData = 6.8813X There is a 27.24% of reference with a coverageData >= 1X There is a 17.08% of reference with a coverageData >= 2X There is a 10.26% of reference with a coverageData >= 3X There is a 6.86% of reference with a coverageData >= 4X There is a 4.51% of reference with a coverageData >= 5X There is a 3.11% of reference with a coverageData >= 6X There is a 2.16% of reference with a coverageData >= 7X There is a 1.53% of reference with a coverageData >= 8X There is a 1.1% of reference with a coverageData >= 9X There is a 0.81% of reference with a coverageData >= 10X There is a 0.6% of reference with a coverageData >= 11X There is a 0.45% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 244402877 0.9805507244854568 9.446995771010426 chr2 243199373 219472441 0.9024383504475565 8.32521436163295 chr3 198022430 180501872 0.911522356331048 2.0859395057406194 chr4 191154276 97532595 0.5102297319260596 5.393933852979432 chr5 180915260 129106512 0.7136297512990336 1.7044352129164004 chr6 171115067 142170968 0.8308500852236466 5.993300702520943 chr7 159138663 118606964 0.7453057714830745 6.788384580651697 chr8 146364022 146349538 0.9999010412545236 3.228290538969332 chr9 141213431 109697235 0.7768187078465646 11.21265515235422 chr10 135534747 126738392 0.935098893865202 16.464755134572087 chr11 135006516 119884630 0.8879914359096563 6.27269208464535 chr12 133851895 110095487 0.8225172082920454 2.095374522921812 chr13 115169878 73305015 0.6364946830976065 1.6090243865947726 chr14 107349540 86910636 0.809604177158095 1.9197876886564085 chr15 102531392 78015721 0.7608959507737884 1.8585192939809863 chr16 90354753 80398187 0.8898058412046127 7.206068264155948 chr17 81195210 75181358 0.9259334140523807 9.967722073490458 chr18 78077248 99685373 1.2767531586154266 8.64358020577862 chr19 59128983 35533242 0.6009445824562888 4.247233420809701 chr20 63025520 76832025 1.2190621354651259 2.8629595282123437 chr21 48129895 25455438 0.5288903705275069 2.863178237422252 chr22 51304566 18593890 0.36242173844721737 1.1949218351278823 chrMT 16571 2959027 178.56659223945448 118.75968804949773 chrX 155270560 77696168 0.5003921413048295 1.8464045112311782 chrY 59373566 3446927 0.05805490948615079 5.837937415067681