BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975309.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 = 52,332,498 number of mapped reads = 52,070,397 (99.5%) number of supplementary alignments = 105,006 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,028,497 number of mapped paired reads (second in pair) = 26,041,900 number of mapped paired reads (both in pair) = 51,984,568 number of mapped paired reads (singletons) = 85,829 number of mapped bases = 4,715,703,735 bp number of sequenced bases = 4,714,067,302 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,078,517 duplication rate = 42.24% >>>>>>> Insert size mean insert size = 37,851.0962 std insert size = 1,913,898.0881 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 55.6587 >>>>>>> ACTG content number of A's = 1,236,772,298 bp (26.24%) number of C's = 1,025,489,133 bp (21.75%) number of T's = 1,295,404,253 bp (27.48%) number of G's = 1,156,320,505 bp (24.53%) number of N's = 81,113 bp (0%) GC percentage = 46.28% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 27,738,807 number of insertions = 509,610 mapped reads with insertion percentage = 0.97% number of deletions = 1,083,825 mapped reads with deletion percentage = 2.05% homopolymer indels = 45.37% >>>>>>> Coverage mean coverageData = 1.5233X std coverageData = 22.9579X There is a 15.17% of reference with a coverageData >= 1X There is a 8.49% of reference with a coverageData >= 2X There is a 4.94% of reference with a coverageData >= 3X There is a 3.52% of reference with a coverageData >= 4X There is a 2.59% of reference with a coverageData >= 5X There is a 2.14% of reference with a coverageData >= 6X There is a 1.82% of reference with a coverageData >= 7X There is a 1.62% of reference with a coverageData >= 8X There is a 1.48% of reference with a coverageData >= 9X There is a 1.38% of reference with a coverageData >= 10X There is a 1.3% of reference with a coverageData >= 11X There is a 1.24% of reference with a coverageData >= 12X There is a 1.19% of reference with a coverageData >= 13X There is a 1.14% of reference with a coverageData >= 14X There is a 1.1% of reference with a coverageData >= 15X There is a 1.06% of reference with a coverageData >= 16X There is a 1.03% of reference with a coverageData >= 17X There is a 1% of reference with a coverageData >= 18X There is a 0.98% of reference with a coverageData >= 19X There is a 0.95% of reference with a coverageData >= 20X There is a 0.93% of reference with a coverageData >= 21X There is a 0.9% of reference with a coverageData >= 22X There is a 0.88% of reference with a coverageData >= 23X There is a 0.86% of reference with a coverageData >= 24X There is a 0.84% of reference with a coverageData >= 25X There is a 0.83% of reference with a coverageData >= 26X There is a 0.81% of reference with a coverageData >= 27X There is a 0.79% of reference with a coverageData >= 28X There is a 0.78% of reference with a coverageData >= 29X There is a 0.76% of reference with a coverageData >= 30X There is a 0.75% of reference with a coverageData >= 31X There is a 0.73% of reference with a coverageData >= 32X There is a 0.72% of reference with a coverageData >= 33X There is a 0.71% of reference with a coverageData >= 34X There is a 0.7% of reference with a coverageData >= 35X There is a 0.68% of reference with a coverageData >= 36X There is a 0.67% of reference with a coverageData >= 37X There is a 0.66% of reference with a coverageData >= 38X There is a 0.65% of reference with a coverageData >= 39X There is a 0.64% of reference with a coverageData >= 40X There is a 0.63% of reference with a coverageData >= 41X There is a 0.62% of reference with a coverageData >= 42X There is a 0.61% of reference with a coverageData >= 43X There is a 0.6% of reference with a coverageData >= 44X There is a 0.59% of reference with a coverageData >= 45X There is a 0.58% of reference with a coverageData >= 46X There is a 0.57% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.56% of reference with a coverageData >= 49X There is a 0.55% of reference with a coverageData >= 50X There is a 0.54% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 564565477 2.265051435919993 30.79793858490692 chr2 243199373 353048199 1.4516821924536787 20.206186622361695 chr3 198022430 235545079 1.189486862675102 17.801995907822565 chr4 191154276 213818680 1.1185660319730435 19.22240327879441 chr5 180915260 238341755 1.3174220626828272 19.672451518392204 chr6 171115067 364816852 2.1319972483779 33.271909974555875 chr7 159138663 252240863 1.5850382191535692 24.501009648744112 chr8 146364022 177677828 1.2139446946873325 17.444577584926513 chr9 141213431 193801792 1.372403394121909 20.982025744497932 chr10 135534747 210468723 1.5528764959438777 22.370065414658754 chr11 135006516 228061816 1.6892652499824528 24.287745281942595 chr12 133851895 259079801 1.935570661887155 25.609540192423587 chr13 115169878 103931722 0.9024210479757563 15.847237241715968 chr14 107349540 154802955 1.4420458159392207 20.751451481520736 chr15 102531392 174952888 1.7063348559629425 23.76390593098823 chr16 90354753 152369377 1.6863460077191512 21.323932694621572 chr17 81195210 186040315 2.2912720467131003 30.97653606172679 chr18 78077248 90461359 1.15861356947417 18.368870108717534 chr19 59128983 174738030 2.955201005232916 32.741996417192254 chr20 63025520 115895667 1.83886887406879 25.837047491669356 chr21 48129895 51519358 1.0704232369507558 21.607982863903494 chr22 51304566 79008591 1.5399914112907611 22.48208922956356 chrMT 16571 219726 13.259670508720053 16.395733273168382 chrX 155270560 128041803 0.8246367051165397 14.176284228911657 chrY 59373566 12255079 0.2064063155647414 4.857421665506767