BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038448.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 = 18,913,608 number of mapped reads = 16,972,784 (89.74%) number of supplementary alignments = 324,952 (1.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,621,333 number of mapped paired reads (second in pair) = 8,351,451 number of mapped paired reads (both in pair) = 16,625,526 number of mapped paired reads (singletons) = 347,258 number of mapped bases = 2,274,447,649 bp number of sequenced bases = 2,272,648,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,433,612 duplication rate = 13.35% >>>>>>> Insert size mean insert size = 97,255.5266 std insert size = 2,957,086.6156 median insert size = 252 >>>>>>> Mapping quality mean mapping quality = 53.2814 >>>>>>> ACTG content number of A's = 652,313,315 bp (28.7%) number of C's = 449,854,283 bp (19.79%) number of T's = 665,879,006 bp (29.3%) number of G's = 504,428,604 bp (22.2%) number of N's = 173,543 bp (0.01%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 31,706,709 number of insertions = 461,254 mapped reads with insertion percentage = 2.54% number of deletions = 841,733 mapped reads with deletion percentage = 4.74% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.7347X std coverageData = 11.4721X There is a 30.01% of reference with a coverageData >= 1X There is a 16.37% of reference with a coverageData >= 2X There is a 8.73% of reference with a coverageData >= 3X There is a 5.09% of reference with a coverageData >= 4X There is a 2.94% of reference with a coverageData >= 5X There is a 1.78% of reference with a coverageData >= 6X There is a 1.09% of reference with a coverageData >= 7X There is a 0.68% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% 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 0.01% 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 165016841 0.6620518750884075 18.848154063141966 chr2 243199373 188965143 0.7769968346094379 11.767057528598599 chr3 198022430 184562193 0.9320267052575811 1.8424739433534705 chr4 191154276 151017623 0.7900300540491179 12.293459648966742 chr5 180915260 141632795 0.782868150536334 1.6827000475678693 chr6 171115067 131437545 0.7681237386302165 6.810398488776023 chr7 159138663 111597758 0.7012611259653476 9.049017385233919 chr8 146364022 109697565 0.7494844942153885 3.1570717235463013 chr9 141213431 97332840 0.689260499590864 18.493791944613005 chr10 135534747 132573903 0.9781543547648338 27.906654387892498 chr11 135006516 111419416 0.8252891734499689 8.671934906101763 chr12 133851895 100777015 0.752899426638674 1.7418020791380457 chr13 115169878 69031016 0.5993842938689229 1.3582676173085675 chr14 107349540 74475662 0.6937678726895337 1.78642620937322 chr15 102531392 55517205 0.5414654372389678 1.285574623353107 chr16 90354753 76990221 0.8520882238480582 14.019521176539664 chr17 81195210 49305010 0.6072403778498756 12.517243425009154 chr18 78077248 62147558 0.7959752628576253 14.622994901611625 chr19 59128983 35258938 0.5963055038507934 9.507415056736436 chr20 63025520 41312250 0.655484476764333 3.6978964738407476 chr21 48129895 29099364 0.6046006125714589 5.331299131779422 chr22 51304566 19970314 0.3892502277477603 1.312128414107737 chrMT 16571 2212757 133.53189306619998 64.63119067106322 chrX 155270560 122951316 0.7918520806519922 3.9774228533796414 chrY 59373566 10145401 0.1708740384567772 12.882742082068155