BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124921.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,278,406 number of mapped reads = 4,210,844 (98.42%) number of supplementary alignments = 53,335 (1.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,109,371 number of mapped paired reads (second in pair) = 2,101,473 number of mapped paired reads (both in pair) = 4,193,582 number of mapped paired reads (singletons) = 17,262 number of mapped bases = 567,685,306 bp number of sequenced bases = 567,280,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 652,239 duplication rate = 14.37% >>>>>>> Insert size mean insert size = 63,577.7379 std insert size = 2,415,012.4048 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.4485 >>>>>>> ACTG content number of A's = 164,152,905 bp (28.94%) number of C's = 115,491,978 bp (20.36%) number of T's = 166,477,785 bp (29.35%) number of G's = 121,132,808 bp (21.35%) number of N's = 24,732 bp (0%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0144 number of mismatches = 7,880,396 number of insertions = 107,534 mapped reads with insertion percentage = 2.42% number of deletions = 207,343 mapped reads with deletion percentage = 4.74% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.1834X std coverageData = 2.1055X There is a 9.45% of reference with a coverageData >= 1X There is a 5.7% of reference with a coverageData >= 2X There is a 1.26% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 42859859 0.1719548734845479 2.1809228150580457 chr2 243199373 50627019 0.20817084507861786 2.0156712490150377 chr3 198022430 39234122 0.198129686621864 0.6915415275995893 chr4 191154276 28286181 0.14797566443138316 1.3514409696620937 chr5 180915260 47187818 0.26082829054884593 0.7686003183887925 chr6 171115067 38047416 0.22234988810190515 1.7646014953761031 chr7 159138663 48087372 0.3021727787168854 3.0373254540531063 chr8 146364022 24114990 0.1647603671344861 0.7550386105226345 chr9 141213431 24704533 0.17494464106604704 2.7446581710314124 chr10 135534747 34171764 0.25212548631532844 5.974312261000631 chr11 135006516 25762621 0.19082501914203903 1.3372056709750344 chr12 133851895 22370409 0.16712807091748683 0.601668358306087 chr13 115169878 12719938 0.11044500715716657 0.4754159809224624 chr14 107349540 12223058 0.11386222987075678 0.520201221640924 chr15 102531392 13878718 0.13536067080801947 0.5367605732532402 chr16 90354753 24555099 0.2717632242323766 3.9572763236745114 chr17 81195210 12541314 0.15445879134988383 2.0167329896505852 chr18 78077248 16264383 0.20831142767736896 2.4655513413110914 chr19 59128983 8851185 0.1496928333774995 1.379776225729315 chr20 63025520 12305955 0.19525352587332878 0.8003082816413694 chr21 48129895 5333715 0.11081916966575556 0.771612034634479 chr22 51304566 4466169 0.08705207641752588 0.45307152180748017 chrMT 16571 20521 1.2383682336612154 1.581642970191162 chrX 155270560 17617289 0.11346187583789226 0.6689560074719524 chrY 59373566 1453858 0.02448662086424117 1.5754605005901816