BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038402.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 = 21,226,912 number of mapped reads = 19,288,447 (90.87%) number of supplementary alignments = 391,739 (1.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,783,638 number of mapped paired reads (second in pair) = 9,504,809 number of mapped paired reads (both in pair) = 18,893,858 number of mapped paired reads (singletons) = 394,589 number of mapped bases = 2,520,289,661 bp number of sequenced bases = 2,518,396,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,541,731 duplication rate = 20.34% >>>>>>> Insert size mean insert size = 87,554.1315 std insert size = 2,847,649.2627 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 53.153 >>>>>>> ACTG content number of A's = 728,255,161 bp (28.92%) number of C's = 480,799,021 bp (19.09%) number of T's = 748,825,119 bp (29.73%) number of G's = 560,326,009 bp (22.25%) number of N's = 191,648 bp (0.01%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 30,978,892 number of insertions = 503,713 mapped reads with insertion percentage = 2.46% number of deletions = 899,390 mapped reads with deletion percentage = 4.47% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 0.8141X std coverageData = 10.984X There is a 24.19% of reference with a coverageData >= 1X There is a 15.79% of reference with a coverageData >= 2X There is a 9.96% of reference with a coverageData >= 3X There is a 7.02% of reference with a coverageData >= 4X There is a 4.83% of reference with a coverageData >= 5X There is a 3.51% of reference with a coverageData >= 6X There is a 2.54% of reference with a coverageData >= 7X There is a 1.9% of reference with a coverageData >= 8X There is a 1.42% of reference with a coverageData >= 9X There is a 1.09% of reference with a coverageData >= 10X There is a 0.84% of reference with a coverageData >= 11X There is a 0.65% of reference with a coverageData >= 12X There is a 0.51% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.18% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% 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 0.02% 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 0.01% 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 196481777 0.7882900199474328 14.854145315235352 chr2 243199373 227132313 0.9339346158593921 14.307376136947669 chr3 198022430 169192298 0.8544097656007958 2.236368355032779 chr4 191154276 174452090 0.912624575554878 11.423638936156987 chr5 180915260 151271010 0.8361428991672676 2.2899010645175673 chr6 171115067 147394802 0.8613782794474785 7.396962228232226 chr7 159138663 132116940 0.8302001381022034 11.266615108077753 chr8 146364022 127906734 0.8738946378502772 4.182577744386091 chr9 141213431 104997153 0.7435351740727835 17.441767781082035 chr10 135534747 133873946 0.9877463083322833 25.973107139829256 chr11 135006516 113218019 0.8386115156101058 6.348951933377576 chr12 133851895 108300594 0.8091076633618075 2.3167558114274307 chr13 115169878 78286983 0.6797522438983569 1.9587716363746541 chr14 107349540 72383402 0.6742777099929818 2.2213331990278222 chr15 102531392 66564407 0.6492100195031001 1.8817184515393357 chr16 90354753 77319122 0.8557283311924941 12.836739276593573 chr17 81195210 59830005 0.7368661895202931 10.803934673133345 chr18 78077248 71597454 0.9170079099099394 16.38680712629681 chr19 59128983 37656875 0.6368598458728776 7.814366986374328 chr20 63025520 49409496 0.7839601482066312 3.9276483417184256 chr21 48129895 33234289 0.690512393596537 5.606909002942697 chr22 51304566 22499988 0.43855722315241885 2.05681631169029 chrMT 16571 4697888 283.5005732906886 244.53346087546095 chrX 155270560 150594496 0.9698844133749501 4.167477621362693 chrY 59373566 9877580 0.16636326004067198 13.675694240269777