BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630574.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 34,830,550 number of mapped reads = 34,486,687 (99.01%) number of supplementary alignments = 71,438 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,299,724 number of mapped paired reads (second in pair) = 17,186,963 number of mapped paired reads (both in pair) = 34,308,218 number of mapped paired reads (singletons) = 178,469 number of mapped bases = 3,356,914,692 bp number of sequenced bases = 3,354,527,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,312,702 duplication rate = 10.26% >>>>>>> Insert size mean insert size = 26,082.0045 std insert size = 1,571,199.3269 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.9351 >>>>>>> ACTG content number of A's = 987,775,292 bp (29.45%) number of C's = 663,321,339 bp (19.77%) number of T's = 997,845,598 bp (29.75%) number of G's = 705,083,803 bp (21.02%) number of N's = 501,827 bp (0.01%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 30,417,731 number of insertions = 607,198 mapped reads with insertion percentage = 1.73% number of deletions = 1,749,774 mapped reads with deletion percentage = 4.94% homopolymer indels = 54.21% >>>>>>> Coverage mean coverageData = 1.0844X std coverageData = 5.0715X There is a 18.15% of reference with a coverageData >= 1X There is a 12.78% of reference with a coverageData >= 2X There is a 9.7% of reference with a coverageData >= 3X There is a 7.77% of reference with a coverageData >= 4X There is a 6.42% of reference with a coverageData >= 5X There is a 5.41% of reference with a coverageData >= 6X There is a 4.63% of reference with a coverageData >= 7X There is a 4.01% of reference with a coverageData >= 8X There is a 3.5% of reference with a coverageData >= 9X There is a 3.08% of reference with a coverageData >= 10X There is a 2.73% of reference with a coverageData >= 11X There is a 2.43% of reference with a coverageData >= 12X There is a 2.18% of reference with a coverageData >= 13X There is a 1.96% of reference with a coverageData >= 14X There is a 1.76% of reference with a coverageData >= 15X There is a 1.6% of reference with a coverageData >= 16X There is a 1.45% of reference with a coverageData >= 17X There is a 1.32% of reference with a coverageData >= 18X There is a 1.2% of reference with a coverageData >= 19X There is a 1.09% of reference with a coverageData >= 20X There is a 1% of reference with a coverageData >= 21X There is a 0.92% of reference with a coverageData >= 22X There is a 0.84% of reference with a coverageData >= 23X There is a 0.78% of reference with a coverageData >= 24X There is a 0.72% of reference with a coverageData >= 25X There is a 0.66% of reference with a coverageData >= 26X There is a 0.61% of reference with a coverageData >= 27X There is a 0.56% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.48% of reference with a coverageData >= 30X There is a 0.45% of reference with a coverageData >= 31X There is a 0.42% of reference with a coverageData >= 32X There is a 0.39% of reference with a coverageData >= 33X There is a 0.36% of reference with a coverageData >= 34X There is a 0.34% of reference with a coverageData >= 35X There is a 0.32% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 247955363 0.9948033910816214 6.2472337827317945 chr2 243199373 283220746 1.1645619908732248 5.742463051773761 chr3 198022430 216302012 1.0923106639990228 4.463342568116566 chr4 191154276 261983161 1.3705325692008061 5.616679450167631 chr5 180915260 235404487 1.301186461551115 4.820687578571909 chr6 171115067 204700626 1.1962747032673633 4.872759507436846 chr7 159138663 166598865 1.0468786268488381 4.274551000038656 chr8 146364022 171056976 1.1687091790904736 4.748920867041729 chr9 141213431 123872860 0.8772031040021965 5.639844562421745 chr10 135534747 153388247 1.1317263682943237 5.027789460886978 chr11 135006516 176424233 1.3067830963062552 5.311429536749505 chr12 133851895 149826168 1.1193428976108257 4.517026801981983 chr13 115169878 104959713 0.9113469148591092 3.9607415359569225 chr14 107349540 117444016 1.0940337145366437 4.508769749349785 chr15 102531392 93383428 0.9107788958917089 4.0272154114924765 chr16 90354753 91947337 1.0176259017608071 5.909506897216921 chr17 81195210 100971156 1.2435605006748551 5.000763105079394 chr18 78077248 89134163 1.1416150707565922 6.670661388695883 chr19 59128983 41230452 0.6972968231163388 4.14259346104501 chr20 63025520 69249342 1.0987508234759507 4.768248315928829 chr21 48129895 46611787 0.9684581069624191 5.736432764994338 chr22 51304566 31154072 0.6072378041361854 3.347702434858354 chrMT 16571 1703 0.1027698992215316 0.568306990784815 chrX 155270560 174899451 1.126417338869648 4.7051874820550905 chrY 59373566 5194328 0.08748553186109792 2.830248451532034