BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038425.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 = 11,461,958 number of mapped reads = 10,787,050 (94.11%) number of supplementary alignments = 229,628 (2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,453,063 number of mapped paired reads (second in pair) = 5,333,987 number of mapped paired reads (both in pair) = 10,648,970 number of mapped paired reads (singletons) = 138,080 number of mapped bases = 1,517,977,631 bp number of sequenced bases = 1,516,797,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,594,901 duplication rate = 8.7% >>>>>>> Insert size mean insert size = 92,434.9553 std insert size = 2,883,570.7632 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 53.6076 >>>>>>> ACTG content number of A's = 441,499,435 bp (29.11%) number of C's = 306,738,754 bp (20.22%) number of T's = 443,286,354 bp (29.23%) number of G's = 325,240,201 bp (21.44%) number of N's = 33,063 bp (0%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 21,078,608 number of insertions = 297,535 mapped reads with insertion percentage = 2.58% number of deletions = 552,470 mapped reads with deletion percentage = 4.91% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.4904X std coverageData = 8.1299X There is a 23.28% of reference with a coverageData >= 1X There is a 11.05% of reference with a coverageData >= 2X There is a 5.08% of reference with a coverageData >= 3X There is a 2.63% of reference with a coverageData >= 4X There is a 1.34% of reference with a coverageData >= 5X There is a 0.72% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 120209679 0.4822843711189791 13.662133853528248 chr2 243199373 138193814 0.568232608066798 8.298372124517458 chr3 198022430 100485091 0.507442975020557 1.1686443722802662 chr4 191154276 103677518 0.5423761381095131 8.362753915488387 chr5 180915260 91629555 0.5064777564921832 1.2449801892856085 chr6 171115067 92874266 0.5427591364587433 10.848615994510343 chr7 159138663 79724314 0.500973883386214 6.460399125879894 chr8 146364022 76609880 0.5234201612743329 2.0834517058326334 chr9 141213431 66419688 0.4703496510894916 14.597432505092819 chr10 135534747 82850011 0.611282441099772 14.337975671540555 chr11 135006516 72143627 0.5343714447086391 6.038898829859284 chr12 133851895 65388320 0.48851247119063945 1.163227993430085 chr13 115169878 45740649 0.39715809197957125 0.9999650151051264 chr14 107349540 43867223 0.40863913343270963 1.1316567198331484 chr15 102531392 40937304 0.3992660511231526 1.0101304129789699 chr16 90354753 51701070 0.572200889088812 8.512004986547064 chr17 81195210 38289462 0.47157291667821294 7.6965106624183335 chr18 78077248 44632083 0.5716400634407606 11.95565507381332 chr19 59128983 22797079 0.3855483020907023 6.917753335340881 chr20 63025520 31268069 0.4961175885577779 2.5030942598285884 chr21 48129895 20195968 0.41961379720441944 3.5377492260356083 chr22 51304566 14477679 0.2821908482765452 0.915582271196382 chrMT 16571 5676394 342.54987628990403 228.7764712882467 chrX 155270560 45317479 0.2918613741072358 1.6405748832848068 chrY 59373566 22871409 0.38521198137231644 10.829252553617877