BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038407.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 = 13,166,426 number of mapped reads = 12,845,078 (97.56%) number of supplementary alignments = 305,774 (2.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,488,378 number of mapped paired reads (second in pair) = 6,356,700 number of mapped paired reads (both in pair) = 12,689,582 number of mapped paired reads (singletons) = 155,496 number of mapped bases = 1,820,986,736 bp number of sequenced bases = 1,819,538,338 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,326,250 duplication rate = 9.23% >>>>>>> Insert size mean insert size = 103,325.4896 std insert size = 3,009,612.3412 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 53.5226 >>>>>>> ACTG content number of A's = 525,488,491 bp (28.88%) number of C's = 375,868,565 bp (20.66%) number of T's = 527,205,023 bp (28.97%) number of G's = 390,936,329 bp (21.49%) number of N's = 39,930 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0162 number of mismatches = 28,142,626 number of insertions = 377,637 mapped reads with insertion percentage = 2.72% number of deletions = 644,070 mapped reads with deletion percentage = 4.79% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.5882X std coverageData = 12.418X There is a 26.02% of reference with a coverageData >= 1X There is a 12.82% of reference with a coverageData >= 2X There is a 6.07% of reference with a coverageData >= 3X There is a 3.28% of reference with a coverageData >= 4X There is a 1.73% of reference with a coverageData >= 5X There is a 0.98% of reference with a coverageData >= 6X There is a 0.56% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% 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 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 111132514 0.44586654811182996 14.850243216522504 chr2 243199373 196958440 0.809864094509816 15.293285160687178 chr3 198022430 103451063 0.5224209348405633 1.2671962347003098 chr4 191154276 110486466 0.577996309117354 15.064465419076694 chr5 180915260 99677639 0.5509631360007995 1.4329315786507675 chr6 171115067 127305857 0.7439780682784644 17.437411224335044 chr7 159138663 120683910 0.7583569430893108 12.47643879460981 chr8 146364022 83422397 0.5699651858432805 3.173108895541573 chr9 141213431 73591782 0.5211386868717891 18.381576986268477 chr10 135534747 85332811 0.6296009908071766 26.531557497584778 chr11 135006516 88403044 0.654805757671726 8.207579689427014 chr12 133851895 57252813 0.4277325547015976 1.120467940226652 chr13 115169878 106300942 0.9229925727628191 1.740873780190196 chr14 107349540 32326247 0.30113074541353413 1.1635571062079395 chr15 102531392 30698833 0.299409111699176 0.8468651675700364 chr16 90354753 75423212 0.8347453730519301 17.558340101209545 chr17 81195210 41334926 0.5090808435620772 6.928342926408638 chr18 78077248 31275152 0.4005667822718342 16.041498881001097 chr19 59128983 23474041 0.3969972052453532 8.213466161063701 chr20 63025520 56920568 0.9031352379163234 4.630228780775115 chr21 48129895 16803014 0.34911802737155356 6.371979296790369 chr22 51304566 10660668 0.2077917977125077 0.8290316194341782 chrMT 16571 1386193 83.65174099330154 44.89510083514413 chrX 155270560 95460149 0.6147987680343266 2.4149513338042743 chrY 59373566 41224055 0.694316642527417 22.447648763125265