BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472832.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,643,584 number of mapped reads = 2,277,604 (86.16%) number of supplementary alignments = 15,475 (0.59%) number of secondary alignments = 0 number of mapped bases = 148,476,103 bp number of sequenced bases = 148,414,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,141 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6073 >>>>>>> ACTG content number of A's = 39,944,667 bp (26.91%) number of C's = 29,100,750 bp (19.61%) number of T's = 44,683,208 bp (30.11%) number of G's = 34,682,454 bp (23.37%) number of N's = 3,420 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,278,448 number of insertions = 11,614 mapped reads with insertion percentage = 0.5% number of deletions = 34,896 mapped reads with deletion percentage = 1.52% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 0.048X std coverageData = 0.3418X There is a 4.12% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% 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 11035504 0.04427473021220677 0.38212027219409034 chr2 243199373 14581980 0.05995895392378335 0.4996412349862433 chr3 198022430 10872113 0.05490344199896951 0.2632064279701508 chr4 191154276 8035871 0.042038667238602605 0.2530398000115921 chr5 180915260 7631449 0.04218245050196429 0.2328059495014651 chr6 171115067 9200721 0.05376920432144061 0.287061262354724 chr7 159138663 9142555 0.057450243879452474 0.47928470739171497 chr8 146364022 8401612 0.05740216677019165 0.3535072758002441 chr9 141213431 8544594 0.0605083662332374 0.41931107654276406 chr10 135534747 6217114 0.045870997198969206 0.29761234419146054 chr11 135006516 4471573 0.03312116431476537 0.3136760917457078 chr12 133851895 6402500 0.04783271839371419 0.2543561844526489 chr13 115169878 5957450 0.05172750117873703 0.2646003533749986 chr14 107349540 3087822 0.028764184737074792 0.21883118252279546 chr15 102531392 2892406 0.028209955444670056 0.205373083466823 chr16 90354753 4825961 0.053411257734277684 0.28444123600689875 chr17 81195210 3318368 0.04086901185427071 0.25086446931773565 chr18 78077248 2592861 0.03320891894140531 0.6640687565448694 chr19 59128983 3041074 0.05143119069035908 0.3355920495950053 chr20 63025520 6399583 0.10153955096284807 0.3814186877169019 chr21 48129895 2257282 0.04689979066025388 0.27888418452387087 chr22 51304566 1724753 0.0336179239875063 0.20709951795519924 chrMT 16571 125556 7.576851125460141 5.857956573741552 chrX 155270560 7356279 0.04737716538151212 0.2776889641807476 chrY 59373566 359122 0.006048516607542151 0.12908990610382207