BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617411.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 = 30,372,911 (94.92%) number of supplementary alignments = 464,111 (1.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,259,270 number of mapped paired reads (second in pair) = 15,113,641 number of mapped paired reads (both in pair) = 29,958,060 number of mapped paired reads (singletons) = 414,851 number of mapped bases = 2,996,469,764 bp number of sequenced bases = 2,995,817,643 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,405,960 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 48,046.5614 std insert size = 2,071,765.4549 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.965 >>>>>>> ACTG content number of A's = 892,707,192 bp (29.8%) number of C's = 602,618,398 bp (20.12%) number of T's = 884,185,455 bp (29.51%) number of G's = 615,012,124 bp (20.53%) number of N's = 1,294,474 bp (0.04%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 29,954,098 number of insertions = 242,790 mapped reads with insertion percentage = 0.79% number of deletions = 289,954 mapped reads with deletion percentage = 0.93% homopolymer indels = 44.91% >>>>>>> Coverage mean coverageData = 0.9679X std coverageData = 2.9569X There is a 29.8% of reference with a coverageData >= 1X There is a 17.15% of reference with a coverageData >= 2X There is a 11.02% of reference with a coverageData >= 3X There is a 7.64% of reference with a coverageData >= 4X There is a 5.56% of reference with a coverageData >= 5X There is a 4.2% of reference with a coverageData >= 6X There is a 3.25% of reference with a coverageData >= 7X There is a 2.58% of reference with a coverageData >= 8X There is a 2.08% of reference with a coverageData >= 9X There is a 1.7% of reference with a coverageData >= 10X There is a 1.41% of reference with a coverageData >= 11X There is a 1.18% of reference with a coverageData >= 12X There is a 1% of reference with a coverageData >= 13X There is a 0.86% of reference with a coverageData >= 14X There is a 0.74% of reference with a coverageData >= 15X There is a 0.64% of reference with a coverageData >= 16X There is a 0.56% of reference with a coverageData >= 17X There is a 0.49% 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 0.34% 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 0.2% 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 0.15% 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 0.09% 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 192777122 0.7734268473497604 2.7647724708076034 chr2 243199373 298778496 1.228533167312072 3.1004094365791475 chr3 198022430 252818038 1.276714147988185 3.4487581250778794 chr4 191154276 143882674 0.7527044490493113 2.3016416267920845 chr5 180915260 191323429 1.057530630638897 2.897256769436176 chr6 171115067 137285273 0.80229798232788 2.6270057208981816 chr7 159138663 224288972 1.4093933414534217 3.267326697069516 chr8 146364022 132648391 0.9062909667787074 3.302557591120387 chr9 141213431 119678347 0.8474997466777788 2.6429189379950517 chr10 135534747 95916724 0.707691024796763 2.43389093171364 chr11 135006516 222623730 1.6489850756536817 3.890045484555211 chr12 133851895 142884447 1.0674816893701804 2.814014657760652 chr13 115169878 129767199 1.1267459969003353 2.8013772053402453 chr14 107349540 87098781 0.8113568162471865 2.9202089664310265 chr15 102531392 68842649 0.671429965566058 2.3752032467676676 chr16 90354753 75785578 0.8387558538287411 3.377834081548268 chr17 81195210 92679863 1.1414449571594187 3.7199335171741734 chr18 78077248 42948961 0.550082925566229 2.02720640179963 chr19 59128983 42830966 0.7243650038763562 2.369750447352643 chr20 63025520 102302839 1.623197063665639 4.804186183971813 chr21 48129895 40997149 0.851802169940325 2.5584174454781174 chr22 51304566 24320645 0.4740444544448539 2.1275221605196726 chrMT 16571 191288 11.54353991913584 5.138294112819228 chrX 155270560 131411549 0.8463391192767 2.593001669479613 chrY 59373566 2386654 0.040197248721762814 0.5833706146356515