BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617391.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,295,212 (94.67%) number of supplementary alignments = 460,650 (1.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,223,390 number of mapped paired reads (second in pair) = 15,071,822 number of mapped paired reads (both in pair) = 29,867,848 number of mapped paired reads (singletons) = 427,364 number of mapped bases = 2,984,887,464 bp number of sequenced bases = 2,984,234,507 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,399,378 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 48,733.0028 std insert size = 2,102,124.9985 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.9623 >>>>>>> ACTG content number of A's = 888,463,223 bp (29.77%) number of C's = 600,341,154 bp (20.12%) number of T's = 879,641,863 bp (29.48%) number of G's = 613,037,527 bp (20.54%) number of N's = 2,750,740 bp (0.09%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 29,889,498 number of insertions = 257,763 mapped reads with insertion percentage = 0.84% number of deletions = 289,745 mapped reads with deletion percentage = 0.94% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 0.9642X std coverageData = 2.9482X There is a 29.77% of reference with a coverageData >= 1X There is a 17.11% of reference with a coverageData >= 2X There is a 10.98% of reference with a coverageData >= 3X There is a 7.61% of reference with a coverageData >= 4X There is a 5.54% of reference with a coverageData >= 5X There is a 4.17% of reference with a coverageData >= 6X There is a 3.23% of reference with a coverageData >= 7X There is a 2.56% of reference with a coverageData >= 8X There is a 2.06% of reference with a coverageData >= 9X There is a 1.69% of reference with a coverageData >= 10X There is a 1.4% of reference with a coverageData >= 11X There is a 1.17% of reference with a coverageData >= 12X There is a 0.99% of reference with a coverageData >= 13X There is a 0.85% of reference with a coverageData >= 14X There is a 0.73% of reference with a coverageData >= 15X There is a 0.63% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.48% of reference with a coverageData >= 18X There is a 0.43% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192027307 0.7704185699902428 2.773432693678767 chr2 243199373 297315754 1.222518587660997 3.0885780694254352 chr3 198022430 251911152 1.272134434467853 3.452354731762082 chr4 191154276 143164817 0.7489490687616112 2.289196373885796 chr5 180915260 190826808 1.0547855830403692 2.8857818674719122 chr6 171115067 136616611 0.7983903077336842 2.613017471286055 chr7 159138663 222998591 1.4012848090850178 3.2480290427367495 chr8 146364022 132193621 0.9031838507416802 3.276875993219002 chr9 141213431 119476714 0.8460718867456737 2.6397573851699767 chr10 135534747 95710525 0.7061696510932359 2.4398252280147092 chr11 135006516 221545413 1.64099792783335 3.868878812966184 chr12 133851895 142695736 1.0660718400736875 2.8095892602475043 chr13 115169878 129386410 1.1234396723073719 2.794627281999636 chr14 107349540 86651694 0.8071920382704947 2.9181884145284225 chr15 102531392 68432989 0.667434506302226 2.3617164192395643 chr16 90354753 75356405 0.8340059874880074 3.364038732497777 chr17 81195210 92474555 1.1389163843532149 3.720031418277087 chr18 78077248 42663885 0.5464317210565618 2.016151415886169 chr19 59128983 42889881 0.7253613849573567 2.3697550993133794 chr20 63025520 102095999 1.6199152184702323 4.801807081736572 chr21 48129895 40713379 0.8459062501590747 2.5338671684152314 chr22 51304566 24264818 0.4729563056824221 2.1017702952263306 chrMT 16571 182769 11.029449037475107 5.063492584293083 chrX 155270560 130957928 0.8434176317777176 2.5755278400805492 chrY 59373566 2333703 0.03930542086692249 0.5604651525220367