BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046447.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 8,482,322 number of mapped reads = 8,442,942 (99.54%) number of supplementary alignments = 49,202 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,225,599 number of mapped paired reads (second in pair) = 4,217,343 number of mapped paired reads (both in pair) = 8,414,976 number of mapped paired reads (singletons) = 27,966 number of mapped bases = 825,575,775 bp number of sequenced bases = 825,373,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,036,251 duplication rate = 28.21% >>>>>>> Insert size mean insert size = 20,503.36 std insert size = 1,536,173.2155 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 44.2037 >>>>>>> ACTG content number of A's = 245,084,032 bp (29.69%) number of C's = 167,677,228 bp (20.32%) number of T's = 245,655,985 bp (29.76%) number of G's = 166,878,494 bp (20.22%) number of N's = 77,878 bp (0.01%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 2,724,564 number of insertions = 67,194 mapped reads with insertion percentage = 0.78% number of deletions = 78,679 mapped reads with deletion percentage = 0.91% homopolymer indels = 50.63% >>>>>>> Coverage mean coverageData = 0.2667X std coverageData = 51.0224X There is a 1.94% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% 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 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 138081968 0.5539884612764917 95.1802703409655 chr2 243199373 13761993 0.05658728815883913 2.9852257793489705 chr3 198022430 8542579 0.043139451424770416 5.309586301580853 chr4 191154276 21695574 0.11349771741438837 16.290639624502045 chr5 180915260 103788802 0.573687382700608 43.952744016172225 chr6 171115067 340966867 1.9926174414553455 160.43391504533764 chr7 159138663 16445046 0.10333784191714618 14.312805366670226 chr8 146364022 30143309 0.20594753128606974 40.0617341714397 chr9 141213431 413655 0.002929289353503492 0.30852855068311263 chr10 135534747 5888900 0.04344937464634069 4.880300202013883 chr11 135006516 18183719 0.1346877138878245 10.225059716856983 chr12 133851895 81987984 0.6125276298852549 68.42675357161596 chr13 115169878 23477509 0.2038511232945823 24.42336773200243 chr14 107349540 7260726 0.06763630286631876 6.241840715205059 chr15 102531392 1018023 0.009928890851301424 0.43235121251556896 chr16 90354753 4143510 0.04585824057313288 1.18801302893762 chr17 81195210 3640520 0.04483663506751199 3.6706277709064947 chr18 78077248 3261722 0.041775575901445705 5.3199119256085154 chr19 59128983 151584 0.002563615883601448 0.26080420805843807 chr20 63025520 186021 0.0029515186863987796 0.13999649652093146 chr21 48129895 168607 0.003503165755919476 0.36037091500538837 chr22 51304566 70158 0.0013674806254086625 0.09213594667441798 chrMT 16571 128211 7.737070786313439 4.309003019283878 chrX 155270560 2038584 0.013129237120030996 0.4252786137541376 chrY 59373566 130204 0.002192962437189641 0.4226714115448987