BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708506.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,867,942 number of mapped reads = 1,932,191 (67.37%) number of supplementary alignments = 371 (0.01%) number of secondary alignments = 0 number of mapped bases = 92,170,862 bp number of sequenced bases = 92,149,772 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,019 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.8052 >>>>>>> ACTG content number of A's = 26,443,345 bp (28.7%) number of C's = 16,918,422 bp (18.36%) number of T's = 29,679,263 bp (32.21%) number of G's = 19,107,347 bp (20.74%) number of N's = 1,395 bp (0%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 476,648 number of insertions = 4,776 mapped reads with insertion percentage = 0.25% number of deletions = 13,952 mapped reads with deletion percentage = 0.72% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 0.3242X There is a 2.44% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% 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 7280908 0.029211193018451896 0.49447810639441975 chr2 243199373 8030725 0.03302115832346328 0.444221870935318 chr3 198022430 6491476 0.03278151874007404 0.22078971721860566 chr4 191154276 6491721 0.033960637113867126 0.2354446591812629 chr5 180915260 5915069 0.03269524638220126 0.21786605592678546 chr6 171115067 5555552 0.03246676109474334 0.26592852860276334 chr7 159138663 5285544 0.033213449832741146 0.39853174444935374 chr8 146364022 4931047 0.03369029446321173 0.6472411000479859 chr9 141213431 3929248 0.02782488869631671 0.24009967992024545 chr10 135534747 4332565 0.03196645211578106 0.25096155134238857 chr11 135006516 4256509 0.031528174536405336 0.28596214651997537 chr12 133851895 4195306 0.03134289581779922 0.21534034328062568 chr13 115169878 3172649 0.027547558919876602 0.22359402334788261 chr14 107349540 2875549 0.026786784554456405 0.19946568711875723 chr15 102531392 2554597 0.024915266926250255 0.1889171122015937 chr16 90354753 2365907 0.026184643546089934 0.19849184623060825 chr17 81195210 2245093 0.027650559682030503 0.2377371733124879 chr18 78077248 2508728 0.03213135790851645 0.3564187889384967 chr19 59128983 1603828 0.02712422772432937 0.3504861174501397 chr20 63025520 1800391 0.02856606339781092 0.207003583008843 chr21 48129895 1226671 0.02548667517350703 0.2114820580971037 chr22 51304566 881874 0.017188996394589907 0.16397637878205637 chrMT 16571 157583 9.509564902540584 6.490145187839917 chrX 155270560 3323506 0.021404611408627625 0.19661800268174903 chrY 59373566 758816 0.012780367613425813 0.1559351835907734