BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089550.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,901,489 number of mapped reads = 13,001,136 (93.52%) number of supplementary alignments = 85,999 (0.62%) number of secondary alignments = 0 number of mapped bases = 827,624,883 bp number of sequenced bases = 827,336,089 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,447,658 duplication rate = 13.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9635 >>>>>>> ACTG content number of A's = 206,594,467 bp (24.97%) number of C's = 153,583,993 bp (18.56%) number of T's = 260,165,824 bp (31.45%) number of G's = 206,862,855 bp (25%) number of N's = 128,950 bp (0.02%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 6,001,130 number of insertions = 51,953 mapped reads with insertion percentage = 0.4% number of deletions = 167,210 mapped reads with deletion percentage = 1.27% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.2673X std coverageData = 1.7812X There is a 13.13% of reference with a coverageData >= 1X There is a 5.89% of reference with a coverageData >= 2X There is a 2.97% of reference with a coverageData >= 3X There is a 1.62% of reference with a coverageData >= 4X There is a 0.93% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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% 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 59490994 0.23867942138447068 2.9317428316378367 chr2 243199373 68170711 0.280307922504389 2.2186938638543694 chr3 198022430 54883569 0.27715834514302246 0.9586463201589247 chr4 191154276 51504843 0.26944122871726917 1.142721891089284 chr5 180915260 47527843 0.26270776163381687 0.9346559367863673 chr6 171115067 50231060 0.29355135629289736 1.8700785902690986 chr7 159138663 45587973 0.2864669850845737 1.991778000450201 chr8 146364022 43139313 0.2947398712506001 1.8338533615747294 chr9 141213431 33048167 0.23402991320280292 1.727585993556936 chr10 135534747 38759963 0.2859780525506127 2.008265078500919 chr11 135006516 37161274 0.27525541063514297 1.6835214181627836 chr12 133851895 53336559 0.3984744407242049 1.9047754604748088 chr13 115169878 25669378 0.22288274022483553 0.8442457034861623 chr14 107349540 22288068 0.20762145790284708 0.9892114488068553 chr15 102531392 21778690 0.21240997098722703 1.9068085126693257 chr16 90354753 25181283 0.27869350713625435 1.2017011263409503 chr17 81195210 23311560 0.28710511371298875 1.3505390967982158 chr18 78077248 21343305 0.27336138947930133 2.982385733330314 chr19 59128983 16716609 0.28271429934791875 2.3410804921822277 chr20 63025520 17795356 0.28235159344976446 1.0822468722757046 chr21 48129895 10432539 0.2167579837853376 1.1005292225242609 chr22 51304566 9734251 0.18973459399305706 0.8094174416071058 chrMT 16571 454240 27.411743407157083 16.60771402384573 chrX 155270560 47887020 0.308410171252039 1.2551949009363044 chrY 59373566 2190315 0.036890406751044734 0.8396982469823114