BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695961.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 = 97,032,106 number of mapped reads = 96,497,722 (99.45%) number of supplementary alignments = 945,372 (0.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 48,349,389 number of mapped paired reads (second in pair) = 48,148,333 number of mapped paired reads (both in pair) = 96,153,054 number of mapped paired reads (singletons) = 344,668 number of mapped bases = 9,579,302,709 bp number of sequenced bases = 9,577,019,488 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,201,309 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 74,063.5428 std insert size = 2,632,642.527 median insert size = 337 >>>>>>> Mapping quality mean mapping quality = 54.0796 >>>>>>> ACTG content number of A's = 2,772,864,112 bp (28.95%) number of C's = 1,994,357,448 bp (20.82%) number of T's = 2,759,635,924 bp (28.82%) number of G's = 2,049,995,868 bp (21.41%) number of N's = 166,136 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 32,343,473 number of insertions = 973,598 mapped reads with insertion percentage = 0.99% number of deletions = 984,700 mapped reads with deletion percentage = 1% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 3.0944X std coverageData = 4.5179X There is a 81.76% of reference with a coverageData >= 1X There is a 65.45% of reference with a coverageData >= 2X There is a 48.69% of reference with a coverageData >= 3X There is a 34.54% of reference with a coverageData >= 4X There is a 23.83% of reference with a coverageData >= 5X There is a 16.21% of reference with a coverageData >= 6X There is a 10.98% of reference with a coverageData >= 7X There is a 7.45% of reference with a coverageData >= 8X There is a 5.09% of reference with a coverageData >= 9X There is a 3.52% of reference with a coverageData >= 10X There is a 2.46% of reference with a coverageData >= 11X There is a 1.75% of reference with a coverageData >= 12X There is a 1.26% of reference with a coverageData >= 13X There is a 0.92% of reference with a coverageData >= 14X There is a 0.69% of reference with a coverageData >= 15X There is a 0.52% of reference with a coverageData >= 16X There is a 0.4% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% 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 826008317 3.3139669369168794 6.5779115787916815 chr2 243199373 847365057 3.484240302708346 4.920221509507705 chr3 198022430 643646551 3.250371945238729 2.8702234147110914 chr4 191154276 569533447 2.9794439283168326 4.270251329139309 chr5 180915260 571459040 3.1587111004345347 2.8429751885371535 chr6 171115067 566380523 3.309939521573515 3.6862760088716895 chr7 159138663 500073034 3.142372975698558 3.3372676515662434 chr8 146364022 485679936 3.3183013787363675 3.2554576964596933 chr9 141213431 399552489 2.82942271263135 4.17592845774043 chr10 135534747 451127043 3.328497326224396 5.296891779433812 chr11 135006516 470186042 3.4826914724619664 3.520100615541173 chr12 133851895 465629646 3.478692968821995 3.344562270847636 chr13 115169878 288481032 2.504830577314669 2.8673031499597608 chr14 107349540 303267025 2.825042613130899 3.1006023367430604 chr15 102531392 303172272 2.9568726814905624 3.258864885988998 chr16 90354753 296195027 3.27813443306076 4.441955849533044 chr17 81195210 294147315 3.6227175839559993 5.2703356937455155 chr18 78077248 251837282 3.2254887108725963 7.106055685982975 chr19 59128983 209606878 3.5449092368120048 5.359612003547985 chr20 63025520 227045166 3.602432252839802 3.616679014083083 chr21 48129895 118935353 2.4711326089533334 6.0776870229131195 chr22 51304566 126036690 2.4566369005051127 3.2966931359870264 chrMT 16571 9484212 572.3379397743045 170.42659992243122 chrX 155270560 298238829 1.9207686827432064 2.2520318569570756 chrY 59373566 56214503 0.9467934433987003 5.101708287850462