BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080724.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,071,492 number of mapped reads = 1,945,927 (93.94%) number of supplementary alignments = 12,679 (0.61%) number of secondary alignments = 0 number of mapped bases = 134,939,967 bp number of sequenced bases = 134,888,559 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,922 duplication rate = 3.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0725 >>>>>>> ACTG content number of A's = 39,199,270 bp (29.06%) number of C's = 24,886,220 bp (18.45%) number of T's = 43,026,263 bp (31.9%) number of G's = 27,774,834 bp (20.59%) number of N's = 1,972 bp (0%) GC percentage = 39.04% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,087,245 number of insertions = 9,740 mapped reads with insertion percentage = 0.5% number of deletions = 28,840 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.15% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.387X There is a 3.57% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 20379190 0.08176184243087603 0.6515313353500413 chr2 243199373 8825300 0.036288333687439236 0.30467519199397924 chr3 198022430 8178725 0.041302013110333005 0.2374363768776783 chr4 191154276 5667215 0.02964733574675567 0.20669895726380152 chr5 180915260 5825648 0.03220097630238599 0.20816626119767664 chr6 171115067 7749341 0.045287309503843985 0.3142287497582658 chr7 159138663 8395059 0.05275310752108053 0.9405995714623943 chr8 146364022 15580367 0.10644943195124824 0.5623445643982764 chr9 141213431 4144806 0.02935135822880757 0.24523259626339103 chr10 135534747 6012687 0.04436269763354485 0.33095949677060915 chr11 135006516 5438856 0.04028587775718914 0.26543743780206547 chr12 133851895 4072466 0.03042516506770412 0.2025757136329141 chr13 115169878 2879246 0.02499999175131539 0.18274566269551612 chr14 107349540 2599587 0.02421609817797077 0.18611920684812697 chr15 102531392 2292460 0.022358615788616233 0.1734046863432609 chr16 90354753 3080092 0.034088876320651336 0.22552257052288177 chr17 81195210 1956957 0.024101877438336573 0.1908234165152839 chr18 78077248 4218195 0.05402591802415987 0.42850683126367256 chr19 59128983 2045542 0.03459457437311242 0.36974238479680843 chr20 63025520 3049062 0.048378212508203025 0.257224742916617 chr21 48129895 1977785 0.041092651459139894 0.24345943494399674 chr22 51304566 1211969 0.023623024118360147 0.17641163713559752 chrMT 16571 23858 1.439744131313741 1.5930561009362834 chrX 155270560 9063077 0.058369577594104126 0.304324993393394 chrY 59373566 272477 0.004589197152146799 0.09734858121417236