BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038463.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 = 11,017,356 number of mapped reads = 10,374,098 (94.16%) number of supplementary alignments = 163,436 (1.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,250,219 number of mapped paired reads (second in pair) = 5,123,879 number of mapped paired reads (both in pair) = 10,231,914 number of mapped paired reads (singletons) = 142,184 number of mapped bases = 1,481,189,196 bp number of sequenced bases = 1,480,168,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,268,463 duplication rate = 8.09% >>>>>>> Insert size mean insert size = 85,763.3342 std insert size = 2,787,449.986 median insert size = 266 >>>>>>> Mapping quality mean mapping quality = 53.8673 >>>>>>> ACTG content number of A's = 428,123,591 bp (28.92%) number of C's = 304,134,752 bp (20.55%) number of T's = 429,651,434 bp (29.03%) number of G's = 318,227,946 bp (21.5%) number of N's = 30,840 bp (0%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0137 number of mismatches = 19,590,786 number of insertions = 249,257 mapped reads with insertion percentage = 2.27% number of deletions = 516,413 mapped reads with deletion percentage = 4.79% homopolymer indels = 47.98% >>>>>>> Coverage mean coverageData = 0.4785X std coverageData = 5.5594X There is a 21.76% of reference with a coverageData >= 1X There is a 10.76% of reference with a coverageData >= 2X There is a 5.33% of reference with a coverageData >= 3X There is a 2.97% of reference with a coverageData >= 4X There is a 1.66% of reference with a coverageData >= 5X There is a 0.98% of reference with a coverageData >= 6X There is a 0.59% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 90122752 0.36157483435116494 3.4011501234912465 chr2 243199373 149589530 0.6150901137397258 6.582875184114019 chr3 198022430 99772204 0.503842943448376 1.2157284061497073 chr4 191154276 84205792 0.44051220700916993 5.143396192273289 chr5 180915260 83110394 0.45938852256023066 1.1926374808209637 chr6 171115067 106027271 0.6196255704355946 6.907316954966515 chr7 159138663 104429855 0.6562192557819843 5.722682660382454 chr8 146364022 65590908 0.4481354577698063 1.53872004538965 chr9 141213431 59815128 0.4235795956264245 7.535044849324321 chr10 135534747 63106231 0.46560924336251575 14.824863022569772 chr11 135006516 85753729 0.6351821492823354 3.33124055886446 chr12 133851895 50972461 0.3808123971647917 1.0340182986580821 chr13 115169878 75636288 0.6567367206901096 1.4888817533699503 chr14 107349540 27154174 0.2529510047271744 0.8708616862919597 chr15 102531392 26465926 0.25812510182247406 0.8120810117497158 chr16 90354753 59988039 0.6639168057932713 11.671272918964554 chr17 81195210 32283833 0.3976076051776946 3.1274379659734244 chr18 78077248 22562160 0.28897227525232444 5.973893836702783 chr19 59128983 17141085 0.2898931138389443 2.079588951939014 chr20 63025520 57741393 0.9161589305411523 2.410925763000014 chr21 48129895 12613873 0.262079794688935 2.6141767944884613 chr22 51304566 9056411 0.17652251458476426 0.7629390901359404 chrMT 16571 881119 53.1723492848953 26.498418208540418 chrX 155270560 76433251 0.49225848737841865 1.4135661226982275 chrY 59373566 20735389 0.349236038812289 9.860665796103165