BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038415.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 12,115,950 number of mapped reads = 11,739,187 (96.89%) number of supplementary alignments = 184,645 (1.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,959,185 number of mapped paired reads (second in pair) = 5,780,002 number of mapped paired reads (both in pair) = 11,545,630 number of mapped paired reads (singletons) = 193,557 number of mapped bases = 1,687,122,311 bp number of sequenced bases = 1,685,989,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,630,783 duplication rate = 8.64% >>>>>>> Insert size mean insert size = 76,719.9995 std insert size = 2,628,346.1765 median insert size = 255 >>>>>>> Mapping quality mean mapping quality = 53.8901 >>>>>>> ACTG content number of A's = 504,218,834 bp (29.91%) number of C's = 334,871,691 bp (19.86%) number of T's = 504,112,661 bp (29.9%) number of G's = 342,750,477 bp (20.33%) number of N's = 35,417 bp (0%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 25,452,968 number of insertions = 298,420 mapped reads with insertion percentage = 2.41% number of deletions = 590,420 mapped reads with deletion percentage = 4.84% homopolymer indels = 47.6% >>>>>>> Coverage mean coverageData = 0.545X std coverageData = 8.2137X There is a 25.45% of reference with a coverageData >= 1X There is a 12.59% of reference with a coverageData >= 2X There is a 5.87% of reference with a coverageData >= 3X There is a 3.12% of reference with a coverageData >= 4X There is a 1.6% of reference with a coverageData >= 5X There is a 0.87% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 129864494 0.5210197410099933 10.579886737224909 chr2 243199373 159830163 0.657198088253295 10.959549540819179 chr3 198022430 118319853 0.5975073278314987 1.2827126218580869 chr4 191154276 120605203 0.6309312327389422 5.660140927957756 chr5 180915260 106534384 0.5888634491087154 1.3885513937419147 chr6 171115067 106654543 0.6232913610114765 10.617687666296478 chr7 159138663 91206976 0.573128957354631 8.117214550725562 chr8 146364022 88050996 0.6015890708441997 2.7081524184247865 chr9 141213431 75061311 0.5315451261856247 18.47410510181616 chr10 135534747 88372562 0.6520288262315493 13.902905336593241 chr11 135006516 78255000 0.5796386894392564 5.300495466801901 chr12 133851895 73178995 0.5467161671487729 1.246405991407059 chr13 115169878 55368007 0.48075076540412764 1.1135797898285866 chr14 107349540 49874251 0.46459678355398637 1.2215850960469192 chr15 102531392 44341214 0.43246476162149444 1.072651640211876 chr16 90354753 52902326 0.5854957735316924 9.576058412110392 chr17 81195210 35847904 0.44150269455550395 5.677186726076538 chr18 78077248 51025697 0.6535283748730488 14.399184559347267 chr19 59128983 19146458 0.32380834285615906 5.7281694755962 chr20 63025520 31512486 0.4999956525547112 1.9081336771416946 chr21 48129895 22338995 0.4641396994529076 2.9083105578035053 chr22 51304566 12648435 0.24653624396705742 0.8396325784588538 chrMT 16571 1494810 90.20638464787882 56.59721119974502 chrX 155270560 52504503 0.3381484745079814 1.6946457385488773 chrY 59373566 22182745 0.37361314966326936 9.095193416883195