BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819104.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 = 2,836,667 number of mapped reads = 2,560,018 (90.25%) number of supplementary alignments = 9,595 (0.34%) number of secondary alignments = 0 number of mapped bases = 146,817,406 bp number of sequenced bases = 146,772,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,967 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2175 >>>>>>> ACTG content number of A's = 37,097,032 bp (25.28%) number of C's = 26,996,958 bp (18.39%) number of T's = 47,684,803 bp (32.49%) number of G's = 34,992,145 bp (23.84%) number of N's = 2,043 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 749,787 number of insertions = 9,998 mapped reads with insertion percentage = 0.39% number of deletions = 26,968 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0474X std coverageData = 0.389X There is a 4.03% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14407834 0.05780460623205428 0.6391534284264553 chr2 243199373 12082324 0.049680736635780716 0.5096858573922444 chr3 198022430 7868658 0.039736195541080876 0.23519291215666427 chr4 191154276 8646870 0.04523503308918917 0.2905965878123793 chr5 180915260 7979107 0.044104112610511684 0.24425288665744027 chr6 171115067 6269486 0.03663900619575481 0.310166215772066 chr7 159138663 7388320 0.046426932718418024 0.5500444333513358 chr8 146364022 13959411 0.09537460647262071 0.4386060303465015 chr9 141213431 6404564 0.04535378791270924 0.354293928919533 chr10 135534747 7311053 0.05394227799015997 0.41810098492459 chr11 135006516 4807074 0.035606236961184895 0.36008959634178517 chr12 133851895 6719878 0.050203831630474864 0.2622370041791808 chr13 115169878 3092616 0.026852646314342712 0.19156836126549978 chr14 107349540 3457948 0.03221204301387784 0.21254959985738106 chr15 102531392 3316943 0.032350511734006306 0.23385972763764365 chr16 90354753 3999040 0.04425932081292945 0.27072781120587514 chr17 81195210 4870692 0.05998743029299389 0.2985091430813307 chr18 78077248 3666983 0.04696608927609744 0.6268813932210552 chr19 59128983 3106085 0.05253066842025678 0.4653943074662061 chr20 63025520 4326444 0.06864590724519211 0.3086991912243549 chr21 48129895 2061095 0.042823592280847485 0.2620194274149113 chr22 51304566 1105108 0.02154014907756943 0.1695890590758744 chrMT 16571 115034 6.941886428097279 4.3122394633636 chrX 155270560 9372660 0.06036340694591428 0.33402416767361154 chrY 59373566 482179 0.00812110561120752 0.21718974261731713