BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124979.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 = 6,042,770 number of mapped reads = 5,934,798 (98.21%) number of supplementary alignments = 50,732 (0.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,975,106 number of mapped paired reads (second in pair) = 2,959,692 number of mapped paired reads (both in pair) = 5,899,682 number of mapped paired reads (singletons) = 35,116 number of mapped bases = 504,433,166 bp number of sequenced bases = 504,102,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,055,898 duplication rate = 12.22% >>>>>>> Insert size mean insert size = 75,029.8931 std insert size = 2,522,114.9452 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 52.2813 >>>>>>> ACTG content number of A's = 145,152,458 bp (28.79%) number of C's = 92,241,261 bp (18.3%) number of T's = 152,236,841 bp (30.2%) number of G's = 114,466,497 bp (22.71%) number of N's = 5,260 bp (0%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 4,144,133 number of insertions = 85,826 mapped reads with insertion percentage = 1.39% number of deletions = 176,714 mapped reads with deletion percentage = 2.91% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.1629X std coverageData = 2.5307X There is a 8.88% of reference with a coverageData >= 1X There is a 3.4% of reference with a coverageData >= 2X There is a 1.39% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% 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 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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% 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 38134149 0.15299520156461316 1.569711699022996 chr2 243199373 44341469 0.18232558930158096 2.80663891845192 chr3 198022430 32762706 0.16544946953736503 0.7357636138850012 chr4 191154276 33526578 0.17539015449489606 1.9825862778350736 chr5 180915260 29695729 0.164141648415949 0.6958611866921127 chr6 171115067 28292778 0.1653435813457619 0.9220649020507091 chr7 159138663 36041356 0.2264776850613606 1.8697998123166037 chr8 146364022 27715251 0.18935835884586447 0.8628061087287114 chr9 141213431 20259876 0.1434698941632542 2.161708963829234 chr10 135534747 32365603 0.23879930214500641 9.206491431565354 chr11 135006516 23406130 0.17337037273075026 1.0856680109045098 chr12 133851895 21579928 0.16122243170333897 0.6532442971604124 chr13 115169878 16549126 0.14369317991289354 0.6113916212076502 chr14 107349540 14059274 0.13096724960349154 0.6982752874864953 chr15 102531392 13195241 0.1286946440754457 0.6008955100723826 chr16 90354753 16705725 0.18489038423911136 3.6947997070698264 chr17 81195210 10941220 0.1347520377125695 1.6085628887057384 chr18 78077248 13606623 0.1742712934759176 2.468067641259649 chr19 59128983 6438245 0.10888475791981743 0.9895553922596597 chr20 63025520 9446989 0.14989148840025437 0.8440242915475359 chr21 48129895 6296794 0.13082916553215002 1.0733171168079703 chr22 51304566 4444370 0.08662718246169357 0.5695532590170761 chrMT 16571 170504 10.289300585359966 7.717246709383806 chrX 155270560 15426236 0.09935068180342752 0.7418609370735968 chrY 59373566 9031266 0.15210920630908376 3.801605445617741