BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960899.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 67,927,788 number of mapped reads = 66,818,198 (98.37%) number of supplementary alignments = 167,043 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 33,448,910 number of mapped paired reads (second in pair) = 33,369,288 number of mapped paired reads (both in pair) = 66,551,788 number of mapped paired reads (singletons) = 266,410 number of mapped bases = 6,594,497,390 bp number of sequenced bases = 6,592,452,044 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,953,727 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 23,520.8604 std insert size = 1,440,565.0875 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.633 >>>>>>> ACTG content number of A's = 1,941,354,510 bp (29.45%) number of C's = 1,351,386,388 bp (20.5%) number of T's = 1,931,508,193 bp (29.3%) number of G's = 1,367,958,868 bp (20.75%) number of N's = 244,085 bp (0%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 41,510,908 number of insertions = 727,909 mapped reads with insertion percentage = 1.05% number of deletions = 805,832 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.7% >>>>>>> Coverage mean coverageData = 2.1302X std coverageData = 23.1212X There is a 72.83% of reference with a coverageData >= 1X There is a 54.25% of reference with a coverageData >= 2X There is a 34.25% of reference with a coverageData >= 3X There is a 20.37% of reference with a coverageData >= 4X There is a 10.89% of reference with a coverageData >= 5X There is a 5.57% of reference with a coverageData >= 6X There is a 2.69% of reference with a coverageData >= 7X There is a 1.29% of reference with a coverageData >= 8X There is a 0.63% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 537135263 2.155000701081503 55.40009004179956 chr2 243199373 564919856 2.3228672386420994 14.592598420519778 chr3 198022430 433900219 2.191167025876816 4.925834609262665 chr4 191154276 443368574 2.319427968223949 20.23279567957428 chr5 180915260 395682608 2.1871157137324957 2.7762954546213265 chr6 171115067 376966340 2.2029991081965914 6.937171400721016 chr7 159138663 351791613 2.2105980179059315 14.318352623633485 chr8 146364022 331344176 2.2638362315569602 23.739066568904274 chr9 141213431 275291224 1.94946912663003 19.961719754474725 chr10 135534747 343418457 2.533803800142852 52.560507380786134 chr11 135006516 297202127 2.2013909832322462 9.304731836958371 chr12 133851895 291465314 2.177521013057006 5.479039303746992 chr13 115169878 208996587 1.814680979344269 1.977002410924605 chr14 107349540 194309671 1.810065241080679 2.527937144969094 chr15 102531392 183215566 1.7869216678536852 2.000283526495383 chr16 90354753 210740228 2.3323646073162303 21.532800488362057 chr17 81195210 176989489 2.179802096700039 8.842950730230985 chr18 78077248 179812652 2.3030096040270274 24.006637001901055 chr19 59128983 128773016 2.1778324176487187 26.907667018038456 chr20 63025520 135887750 2.1560750311937134 7.680020075926089 chr21 48129895 90628314 1.882994218042653 10.08430226808399 chr22 51304566 77355345 1.507767261884644 2.2425741538860406 chrMT 16571 5106268 308.1448313318448 48.9883514527942 chrX 155270560 338164589 2.177905386571672 7.263412132560333 chrY 59373566 22032144 0.3710766505080729 21.48322834926827