BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124906.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 = 4,470,756 number of mapped reads = 4,409,247 (98.62%) number of supplementary alignments = 22,511 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,206,354 number of mapped paired reads (second in pair) = 2,202,893 number of mapped paired reads (both in pair) = 4,393,106 number of mapped paired reads (singletons) = 16,141 number of mapped bases = 402,014,059 bp number of sequenced bases = 401,767,225 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 216,964 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 78,859.9922 std insert size = 2,658,117.8046 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.9712 >>>>>>> ACTG content number of A's = 115,522,551 bp (28.75%) number of C's = 81,066,818 bp (20.18%) number of T's = 117,988,179 bp (29.37%) number of G's = 86,927,111 bp (21.64%) number of N's = 262,566 bp (0.07%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 3,499,213 number of insertions = 69,249 mapped reads with insertion percentage = 1.53% number of deletions = 144,206 mapped reads with deletion percentage = 3.2% homopolymer indels = 44.96% >>>>>>> Coverage mean coverageData = 0.1299X std coverageData = 1.1738X There is a 8.76% of reference with a coverageData >= 1X There is a 2.68% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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% 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 30664053 0.12302498134999632 1.0514152329416009 chr2 243199373 32452583 0.1334402412295693 1.5657076239165812 chr3 198022430 35862189 0.18110165095943928 0.5693278543051694 chr4 191154276 21209402 0.1109543686064339 0.8749981811841444 chr5 180915260 19188253 0.10606210332948143 0.441451862822515 chr6 171115067 20004436 0.1169063388205318 0.743326217448789 chr7 159138663 26467618 0.16631796133664892 1.8112002708799766 chr8 146364022 24280348 0.1658901393130615 0.6572047546572314 chr9 141213431 16239325 0.11499844515497963 1.2575484210164183 chr10 135534747 18641962 0.13754378425187158 2.3616863671172963 chr11 135006516 18165476 0.1345525870766119 0.9055483165413514 chr12 133851895 22039655 0.16465702633496523 0.5371630617988961 chr13 115169878 12803428 0.1111699362918488 0.4354201501565351 chr14 107349540 10699995 0.09967434420305853 0.46346056166551713 chr15 102531392 10482310 0.102235128144949 0.41674309854458463 chr16 90354753 18916443 0.2093574756382766 2.9866520539253396 chr17 81195210 10072394 0.12405157890471617 1.0199298703361177 chr18 78077248 9781734 0.125282771237019 1.3765735403712922 chr19 59128983 5628920 0.09519730789213811 0.7105448285200416 chr20 63025520 11886233 0.18859396955392038 0.6127401565659841 chr21 48129895 4619412 0.09597801948248588 0.5495258344180668 chr22 51304566 4262381 0.08307995432609254 0.4180301341528591 chrMT 16571 110448 6.665137891497194 4.817987175513024 chrX 155270560 13677126 0.088085764616293 0.580646882174299 chrY 59373566 3857935 0.06497731667321448 1.3290984788954099