BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926929.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 12,263,204 number of mapped reads = 11,854,287 (96.67%) number of supplementary alignments = 300,023 (2.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,954,213 number of mapped paired reads (second in pair) = 5,900,074 number of mapped paired reads (both in pair) = 11,637,770 number of mapped paired reads (singletons) = 216,517 number of mapped bases = 1,041,958,486 bp number of sequenced bases = 1,041,112,540 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 978,561 duplication rate = 6.9% >>>>>>> Insert size mean insert size = 252,593.7321 std insert size = 5,026,413.1315 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 52.7026 >>>>>>> ACTG content number of A's = 293,306,588 bp (28.17%) number of C's = 198,059,979 bp (19.02%) number of T's = 305,066,807 bp (29.3%) number of G's = 244,628,354 bp (23.5%) number of N's = 50,812 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 9,971,696 number of insertions = 185,971 mapped reads with insertion percentage = 1.54% number of deletions = 570,138 mapped reads with deletion percentage = 4.69% homopolymer indels = 51.85% >>>>>>> Coverage mean coverageData = 0.3366X std coverageData = 1.4781X There is a 19% of reference with a coverageData >= 1X There is a 7.65% of reference with a coverageData >= 2X There is a 3.18% of reference with a coverageData >= 3X There is a 1.54% of reference with a coverageData >= 4X There is a 0.79% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 85501528 0.34303436299161716 1.4709293137119708 chr2 243199373 92157897 0.3789396981710146 3.5159525815337735 chr3 198022430 68878723 0.34783293488520467 0.9205279572447853 chr4 191154276 59843901 0.3130659813228557 1.1753710210072126 chr5 180915260 62956591 0.34798939017084574 0.9139771370477228 chr6 171115067 59281732 0.34644367114673774 1.1071317883579053 chr7 159138663 53717782 0.33755330720605586 1.0871115722785365 chr8 146364022 53345887 0.3644740440379535 0.9858368089036699 chr9 141213431 45429321 0.32170679997145596 1.2392480217829682 chr10 135534747 52598499 0.3880812866386212 1.7368205676102961 chr11 135006516 49318120 0.3653017755083762 1.0583539156194455 chr12 133851895 46024433 0.343845957504001 0.9562867658728507 chr13 115169878 30409275 0.26403844067630255 0.7973859451852955 chr14 107349540 32481551 0.3025774586458405 0.9237190459051003 chr15 102531392 31767372 0.309830690682518 0.8836172410784294 chr16 90354753 32976663 0.3649687692688397 1.686063249883479 chr17 81195210 28593410 0.35215636488901253 0.9814525300946523 chr18 78077248 26875681 0.34421911233346747 1.229442336782811 chr19 59128983 18679765 0.3159155468647245 1.0641427410075865 chr20 63025520 26046922 0.4132757968518149 1.0453769084533993 chr21 48129895 12517287 0.26007301698871355 1.2096258723834767 chr22 51304566 13934013 0.2715940136790164 0.8639882138567219 chrMT 16571 391567 23.62965421519522 18.806946565019988 chrX 155270560 56420105 0.36336640377931273 0.9804101762518233 chrY 59373566 1810461 0.030492711183963583 1.1611842449519425