BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818759.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 369,515 number of mapped reads = 343,645 (93%) number of supplementary alignments = 2,586 (0.7%) number of secondary alignments = 0 number of mapped bases = 23,327,373 bp number of sequenced bases = 23,317,386 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,337 duplication rate = 13.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4089 >>>>>>> ACTG content number of A's = 6,281,561 bp (26.94%) number of C's = 4,832,281 bp (20.72%) number of T's = 6,973,817 bp (29.91%) number of G's = 5,228,349 bp (22.42%) number of N's = 1,378 bp (0.01%) GC percentage = 43.15% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 119,592 number of insertions = 2,978 mapped reads with insertion percentage = 0.85% number of deletions = 6,119 mapped reads with deletion percentage = 1.77% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.0075X std coverageData = 0.124X There is a 0.61% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 1921120 0.007707583605177858 0.15402420843314932 chr2 243199373 2071015 0.008515708632192896 0.17931826775537885 chr3 198022430 1590623 0.008032539546151414 0.10789231281507435 chr4 191154276 1527037 0.007988505577557679 0.11223039435800675 chr5 180915260 1467566 0.008111897249574193 0.11039829659539205 chr6 171115067 1357202 0.007931516632606057 0.11157809512399018 chr7 159138663 1286070 0.008081442785528492 0.11632746490733858 chr8 146364022 1204071 0.008226550374517584 0.11598286736763393 chr9 141213431 1021696 0.007235119158035329 0.11324043737339684 chr10 135534747 1107749 0.008173173481483682 0.13078159440999654 chr11 135006516 1084830 0.008035389936290186 0.11251022601036446 chr12 133851895 1070961 0.00800108956246006 0.110647339830598 chr13 115169878 756629 0.0065696778805305325 0.0974312434608872 chr14 107349540 708173 0.006596889003902579 0.10369538034094777 chr15 102531392 655091 0.006389174936784239 0.09549855941280037 chr16 90354753 698680 0.007732631397929891 0.13948028852068572 chr17 81195210 634739 0.007817443910792275 0.10873986567962829 chr18 78077248 631955 0.008093971242429037 0.1358970641084766 chr19 59128983 470219 0.00795242833789311 0.13863016721219004 chr20 63025520 501540 0.007957728869194575 0.11096154153311825 chr21 48129895 331283 0.006883102487549578 0.10420685684198736 chr22 51304566 289169 0.0056363209465605845 0.09553570963413298 chrMT 16571 1933 0.11664956852332388 0.37332421890949 chrX 155270560 725475 0.004672328096195441 0.08604041116071966 chrY 59373566 212547 0.0035798254058043272 0.17525103082137494