BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777287.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 288,139,362 number of mapped reads = 282,064,577 (97.89%) number of supplementary alignments = 14,278,224 (4.96%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 141,407,643 number of mapped paired reads (second in pair) = 140,656,934 number of mapped paired reads (both in pair) = 280,724,582 number of mapped paired reads (singletons) = 1,339,995 number of mapped bases = 27,147,605,328 bp number of sequenced bases = 27,139,174,600 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,265,506 duplication rate = 22.85% >>>>>>> Insert size mean insert size = 159,437.7178 std insert size = 3,819,175.7383 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 52.9838 >>>>>>> ACTG content number of A's = 7,932,554,981 bp (29.23%) number of C's = 5,660,620,657 bp (20.86%) number of T's = 7,769,668,395 bp (28.63%) number of G's = 5,774,613,223 bp (21.28%) number of N's = 1,717,344 bp (0.01%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 134,540,855 number of insertions = 6,146,924 mapped reads with insertion percentage = 2.13% number of deletions = 3,376,707 mapped reads with deletion percentage = 1.16% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 8.7695X std coverageData = 83.4087X There is a 63.86% of reference with a coverageData >= 1X There is a 56.09% of reference with a coverageData >= 2X There is a 49.33% of reference with a coverageData >= 3X There is a 44.26% of reference with a coverageData >= 4X There is a 39.92% of reference with a coverageData >= 5X There is a 36.25% of reference with a coverageData >= 6X There is a 33.06% of reference with a coverageData >= 7X There is a 30.28% of reference with a coverageData >= 8X There is a 27.83% of reference with a coverageData >= 9X There is a 25.67% of reference with a coverageData >= 10X There is a 23.74% of reference with a coverageData >= 11X There is a 22.01% of reference with a coverageData >= 12X There is a 20.46% of reference with a coverageData >= 13X There is a 19.07% of reference with a coverageData >= 14X There is a 17.8% of reference with a coverageData >= 15X There is a 16.66% of reference with a coverageData >= 16X There is a 15.61% of reference with a coverageData >= 17X There is a 14.65% of reference with a coverageData >= 18X There is a 13.78% of reference with a coverageData >= 19X There is a 12.97% of reference with a coverageData >= 20X There is a 12.23% of reference with a coverageData >= 21X There is a 11.54% of reference with a coverageData >= 22X There is a 10.9% of reference with a coverageData >= 23X There is a 10.31% of reference with a coverageData >= 24X There is a 9.76% of reference with a coverageData >= 25X There is a 9.25% of reference with a coverageData >= 26X There is a 8.77% of reference with a coverageData >= 27X There is a 8.32% of reference with a coverageData >= 28X There is a 7.9% of reference with a coverageData >= 29X There is a 7.5% of reference with a coverageData >= 30X There is a 7.13% of reference with a coverageData >= 31X There is a 6.78% of reference with a coverageData >= 32X There is a 6.45% of reference with a coverageData >= 33X There is a 6.14% of reference with a coverageData >= 34X There is a 5.85% of reference with a coverageData >= 35X There is a 5.57% of reference with a coverageData >= 36X There is a 5.31% of reference with a coverageData >= 37X There is a 5.06% of reference with a coverageData >= 38X There is a 4.83% of reference with a coverageData >= 39X There is a 4.61% of reference with a coverageData >= 40X There is a 4.4% of reference with a coverageData >= 41X There is a 4.2% of reference with a coverageData >= 42X There is a 4.01% of reference with a coverageData >= 43X There is a 3.83% of reference with a coverageData >= 44X There is a 3.66% of reference with a coverageData >= 45X There is a 3.5% of reference with a coverageData >= 46X There is a 3.34% of reference with a coverageData >= 47X There is a 3.19% of reference with a coverageData >= 48X There is a 3.05% of reference with a coverageData >= 49X There is a 2.92% of reference with a coverageData >= 50X There is a 2.79% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2256697970 9.053931183585696 194.8229277757779 chr2 243199373 2351998132 9.67106988388494 60.8815335836163 chr3 198022430 1840729735 9.295561795701628 24.142525919354103 chr4 191154276 1785739093 9.341873644511097 63.933960603971656 chr5 180915260 1660967517 9.180914407109716 17.453964463149184 chr6 171115067 1571428367 9.183459963814876 46.18893677216464 chr7 159138663 1447856407 9.098080753638103 71.60990947512086 chr8 146364022 1371108007 9.367793999265748 34.9756998536278 chr9 141213431 1176143822 8.32883822502691 84.0470484318133 chr10 135534747 1431354367 10.560792702110552 175.1175772015821 chr11 135006516 1290677276 9.560110980124842 45.666451184526274 chr12 133851895 1222427276 9.132685614947775 16.94310937786386 chr13 115169878 853591526 7.411586612951001 14.584801031228185 chr14 107349540 840150281 7.826305366562353 16.846883863745543 chr15 102531392 775677256 7.565266021161597 15.004281261712995 chr16 90354753 802019499 8.876339897691935 33.08922628218023 chr17 81195210 768589353 9.46594451815569 48.09393489096347 chr18 78077248 762389310 9.764551511856565 111.40170687654748 chr19 59128983 522121474 8.830212317367272 109.87776588003933 chr20 63025520 608089897 9.648312255099205 23.527999084736425 chr21 48129895 370858159 7.705359818466257 34.201523467439344 chr22 51304566 331847599 6.46818840646659 15.115096538536953 chrMT 16571 121016322 7302.897954257438 1428.8999353801983 chrX 155270560 752455058 4.846089677270437 22.256552556025962 chrY 59373566 231671625 3.901932132558789 63.65119977719264