BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054608.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 = 12,218,012 number of mapped reads = 9,007,335 (73.72%) number of supplementary alignments = 197 (0%) number of secondary alignments = 0 number of mapped bases = 426,553,401 bp number of sequenced bases = 426,465,104 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,862,753 duplication rate = 14.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1163 >>>>>>> ACTG content number of A's = 129,708,810 bp (30.41%) number of C's = 77,016,561 bp (18.06%) number of T's = 135,033,064 bp (31.66%) number of G's = 84,703,441 bp (19.86%) number of N's = 3,228 bp (0%) GC percentage = 37.92% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 2,333,798 number of insertions = 17,567 mapped reads with insertion percentage = 0.19% number of deletions = 60,402 mapped reads with deletion percentage = 0.67% homopolymer indels = 49.92% >>>>>>> Coverage mean coverageData = 0.1378X std coverageData = 1.0224X There is a 6.1% of reference with a coverageData >= 1X There is a 2.37% of reference with a coverageData >= 2X There is a 1.33% of reference with a coverageData >= 3X There is a 0.86% of reference with a coverageData >= 4X There is a 0.6% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 38107630 0.1528888066441367 1.14809500004425 chr2 243199373 32021699 0.1316685096881397 1.0479819718804682 chr3 198022430 32663808 0.16495004126552734 1.055483849759557 chr4 191154276 26549522 0.13889054723526037 0.9951731471588612 chr5 180915260 21840739 0.1207235862801181 0.8489146438769629 chr6 171115067 21302094 0.12448987908236041 0.9586072033709957 chr7 159138663 27839244 0.17493702331783445 1.2356793343369896 chr8 146364022 23674730 0.16175238748221882 1.1383329959112503 chr9 141213431 21446215 0.15187092933107757 1.0762145211781284 chr10 135534747 18105236 0.1335837222612737 1.030877826628438 chr11 135006516 19176361 0.14204026270850512 1.0225804791641986 chr12 133851895 16804576 0.12554604475341943 0.8727052297102399 chr13 115169878 12861524 0.11167437374553787 0.8278834892824299 chr14 107349540 8825259 0.08221049666351621 0.8505744509326307 chr15 102531392 11358653 0.11078219829493781 0.8031702172438189 chr16 90354753 10866112 0.12026054678053295 0.9214368545942189 chr17 81195210 7475330 0.09206614528123026 0.709650604930429 chr18 78077248 16832396 0.21558644075160027 1.3828684128284718 chr19 59128983 6638092 0.11226460634372826 0.9729410204563443 chr20 63025520 7424394 0.11779980553908956 0.8646749015819899 chr21 48129895 5199816 0.10803713575523072 0.9018619063202932 chr22 51304566 3485586 0.067939099221695 0.5675983776345371 chrMT 16571 34901 2.1061492969645768 4.898532905520788 chrX 155270560 34909148 0.2248278617659394 1.384751985893501 chrY 59373566 1110336 0.018700847444467122 0.38046274278073355