BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1954925.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 = 14,979,714 number of mapped reads = 14,646,020 (97.77%) number of supplementary alignments = 39,148 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,437,843 number of mapped paired reads (second in pair) = 7,208,177 number of mapped paired reads (both in pair) = 14,389,510 number of mapped paired reads (singletons) = 256,510 number of mapped bases = 1,318,636,253 bp number of sequenced bases = 1,317,802,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 834,879 duplication rate = 4.72% >>>>>>> Insert size mean insert size = 42,293.7629 std insert size = 2,083,577.1559 median insert size = 319 >>>>>>> Mapping quality mean mapping quality = 54.1422 >>>>>>> ACTG content number of A's = 373,004,972 bp (28.31%) number of C's = 253,755,478 bp (19.26%) number of T's = 373,948,627 bp (28.38%) number of G's = 317,032,835 bp (24.06%) number of N's = 61,046 bp (0%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 10,486,117 number of insertions = 205,614 mapped reads with insertion percentage = 1.39% number of deletions = 599,889 mapped reads with deletion percentage = 4.01% homopolymer indels = 53.98% >>>>>>> Coverage mean coverageData = 0.426X std coverageData = 1.2676X There is a 22.87% of reference with a coverageData >= 1X There is a 9.1% of reference with a coverageData >= 2X There is a 4.35% of reference with a coverageData >= 3X There is a 2.32% of reference with a coverageData >= 4X There is a 1.33% of reference with a coverageData >= 5X There is a 0.81% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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% 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 113665905 0.4560305789569126 1.3240666237352385 chr2 243199373 132284080 0.5439326523263692 2.1111816366702687 chr3 198022430 87470119 0.44171823868639526 1.09782914625821 chr4 191154276 77307584 0.40442508332902793 1.1287362989213998 chr5 180915260 80086229 0.44267260263175146 1.0942230974435079 chr6 171115067 76210800 0.44537749560066503 1.1141699664559264 chr7 159138663 64796187 0.40716809968423573 1.0597772249299966 chr8 146364022 68195776 0.46593264566069387 1.194128417301178 chr9 141213431 55192817 0.3908467955856125 1.3281704526830285 chr10 135534747 64279916 0.4742689046374211 1.2316095903906001 chr11 135006516 64216931 0.47565801194366053 1.293317675387748 chr12 133851895 63652165 0.4755417545638782 1.1781584567882992 chr13 115169878 38441085 0.3337772485961998 0.9524643487089605 chr14 107349540 44451331 0.414080311848565 1.1293641779365218 chr15 102531392 42087947 0.4104883994942739 1.1060380765720939 chr16 90354753 41293923 0.4570199312038405 1.4593034531454323 chr17 81195210 37761110 0.46506573478903496 1.2046492066538417 chr18 78077248 35577542 0.4556710554142482 1.3656972516389065 chr19 59128983 22865505 0.3867055349150855 1.1417037890929722 chr20 63025520 27610642 0.4380866988483395 1.1246193078645748 chr21 48129895 17061017 0.35447858342512484 1.4364763593053467 chr22 51304566 19205896 0.3743506182276252 1.0924945357270075 chrMT 16571 263394 15.89487659163599 12.443772970009933 chrX 155270560 37725813 0.24296822913500152 0.7570231858128637 chrY 59373566 6932539 0.11676137155043037 0.7675949525399197