BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617394.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,445,755 (95.14%) number of supplementary alignments = 465,402 (1.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,268,508 number of mapped paired reads (second in pair) = 15,177,247 number of mapped paired reads (both in pair) = 30,030,166 number of mapped paired reads (singletons) = 415,589 number of mapped bases = 3,002,296,822 bp number of sequenced bases = 3,001,638,192 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,415,445 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 48,231.2447 std insert size = 2,088,149.3384 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.9846 >>>>>>> ACTG content number of A's = 893,103,583 bp (29.75%) number of C's = 604,363,478 bp (20.13%) number of T's = 884,842,986 bp (29.48%) number of G's = 616,975,093 bp (20.55%) number of N's = 2,353,052 bp (0.08%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 28,939,628 number of insertions = 244,404 mapped reads with insertion percentage = 0.79% number of deletions = 292,451 mapped reads with deletion percentage = 0.94% homopolymer indels = 45.04% >>>>>>> Coverage mean coverageData = 0.9698X std coverageData = 2.9672X There is a 29.83% of reference with a coverageData >= 1X There is a 17.17% of reference with a coverageData >= 2X There is a 11.04% of reference with a coverageData >= 3X There is a 7.66% of reference with a coverageData >= 4X There is a 5.58% of reference with a coverageData >= 5X There is a 4.21% of reference with a coverageData >= 6X There is a 3.26% of reference with a coverageData >= 7X There is a 2.58% of reference with a coverageData >= 8X There is a 2.08% of reference with a coverageData >= 9X There is a 1.71% of reference with a coverageData >= 10X There is a 1.41% of reference with a coverageData >= 11X There is a 1.19% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.86% of reference with a coverageData >= 14X There is a 0.74% of reference with a coverageData >= 15X There is a 0.64% of reference with a coverageData >= 16X There is a 0.56% of reference with a coverageData >= 17X There is a 0.49% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 193705947 0.7771533175036703 2.776455768157211 chr2 243199373 299616229 1.2319778020151393 3.107233558281739 chr3 198022430 253168002 1.2784814427335327 3.4709353065111457 chr4 191154276 143682429 0.7516568920488077 2.298785699022973 chr5 180915260 192333182 1.0631119895579841 2.9180919042211393 chr6 171115067 137108474 0.801264765305559 2.6299634320705714 chr7 159138663 224479348 1.410589631508969 3.2752159316295657 chr8 146364022 132709561 0.9067088973545698 3.3144027335643598 chr9 141213431 119730909 0.8478719633970228 2.6473573822309637 chr10 135534747 96218324 0.7099162844196699 2.4379124478064282 chr11 135006516 223013917 1.6518752102305936 3.8985080229242697 chr12 133851895 143074976 1.0689051208427045 2.8114952179634978 chr13 115169878 129723874 1.1263698134680666 2.7898533152823024 chr14 107349540 87257547 0.8128357792683601 2.947400369675178 chr15 102531392 69184723 0.6747662511009311 2.3901519591728597 chr16 90354753 75880949 0.8398113710741925 3.383476835437265 chr17 81195210 92893953 1.1440816890553027 3.751428174900902 chr18 78077248 42951102 0.5501103471269889 2.034074324895875 chr19 59128983 43085984 0.7286779141795826 2.3835149456636944 chr20 63025520 102880511 1.632362747661582 4.849476404771092 chr21 48129895 41027399 0.852430677440705 2.5553376933623992 chr22 51304566 24385053 0.4752998592756832 2.1238713979910875 chrMT 16571 192995 11.646551203910446 6.052793941896535 chrX 155270560 131641618 0.8478208489748476 2.597764952460883 chrY 59373566 2349816 0.03957680426336528 0.5700128893659689