BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975280.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 2,349,142 number of mapped reads = 2,320,899 (98.8%) number of supplementary alignments = 34,080 (1.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,162,366 number of mapped paired reads (second in pair) = 1,158,533 number of mapped paired reads (both in pair) = 2,312,674 number of mapped paired reads (singletons) = 8,225 number of mapped bases = 309,931,904 bp number of sequenced bases = 309,701,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 392,971 duplication rate = 15.62% >>>>>>> Insert size mean insert size = 86,513.1318 std insert size = 2,754,292.4182 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 53.4755 >>>>>>> ACTG content number of A's = 91,401,402 bp (29.51%) number of C's = 61,975,856 bp (20.01%) number of T's = 91,492,474 bp (29.54%) number of G's = 64,812,342 bp (20.93%) number of N's = 19,395 bp (0.01%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 3,085,910 number of insertions = 63,952 mapped reads with insertion percentage = 2.59% number of deletions = 102,321 mapped reads with deletion percentage = 4.23% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 0.1001X std coverageData = 1.4747X There is a 5.54% of reference with a coverageData >= 1X There is a 3.07% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% 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% 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 27624673 0.11083090942429387 1.4161092373135682 chr2 243199373 25370694 0.10432055678038282 1.6339012933320092 chr3 198022430 21552958 0.10884099341675586 0.503801576072481 chr4 191154276 21427256 0.11209404491689215 1.4341194183946018 chr5 180915260 17870335 0.09877737787293343 0.4391319577910728 chr6 171115067 24427949 0.14275744052392533 0.9792735812470839 chr7 159138663 17904024 0.11250580884922981 1.2797538535153619 chr8 146364022 15618765 0.10671177784387477 0.6363213124334683 chr9 141213431 13545284 0.09592064936089542 2.410507451999309 chr10 135534747 17450054 0.12874967037050655 4.003727397805673 chr11 135006516 10779082 0.07984119818335286 1.1706270324010617 chr12 133851895 11710049 0.08748511928053017 0.4117966692520352 chr13 115169878 9861238 0.08562341274686425 0.4095589186035036 chr14 107349540 9042266 0.08423199577753197 0.42664046274409156 chr15 102531392 8296686 0.08091849567398832 0.3941595771532509 chr16 90354753 9582548 0.10605471966704397 1.8287326912616848 chr17 81195210 5838370 0.07190535008161196 0.7886346824851336 chr18 78077248 8746688 0.11202607960772387 2.1559947182229395 chr19 59128983 4065597 0.06875810801616528 0.9136165244118208 chr20 63025520 5967444 0.09468297921223022 0.6344721778922118 chr21 48129895 4080186 0.08477446294034092 0.8746273320563809 chr22 51304566 2525380 0.049223299150410904 0.31830407948303524 chrMT 16571 65881 3.9756804055277293 3.1937432150897194 chrX 155270560 10114160 0.06513894198616918 0.49084929558784185 chrY 59373566 6464337 0.10887567372995585 2.8851243546883993