BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038438.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 = 14,556,840 number of mapped reads = 14,224,308 (97.72%) number of supplementary alignments = 213,993 (1.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,174,458 number of mapped paired reads (second in pair) = 7,049,850 number of mapped paired reads (both in pair) = 14,086,124 number of mapped paired reads (singletons) = 138,184 number of mapped bases = 2,032,136,535 bp number of sequenced bases = 2,030,878,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,987,140 duplication rate = 9.25% >>>>>>> Insert size mean insert size = 84,108.9135 std insert size = 2,716,429.3061 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 53.6079 >>>>>>> ACTG content number of A's = 593,344,965 bp (29.22%) number of C's = 411,200,418 bp (20.25%) number of T's = 594,298,610 bp (29.26%) number of G's = 431,992,385 bp (21.27%) number of N's = 42,069 bp (0%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0131 number of mismatches = 25,920,595 number of insertions = 311,845 mapped reads with insertion percentage = 2.1% number of deletions = 671,114 mapped reads with deletion percentage = 4.56% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 0.6564X std coverageData = 9.4689X There is a 26.87% of reference with a coverageData >= 1X There is a 14.46% of reference with a coverageData >= 2X There is a 7.78% of reference with a coverageData >= 3X There is a 4.62% of reference with a coverageData >= 4X There is a 2.75% of reference with a coverageData >= 5X There is a 1.71% of reference with a coverageData >= 6X There is a 1.09% of reference with a coverageData >= 7X There is a 0.71% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% 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 0.02% 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 0.01% 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 139774209 0.5607777763570747 15.052267011512813 chr2 243199373 173240771 0.7123405330489894 9.29137970001974 chr3 198022430 134114341 0.6772684336819824 1.4868454631149761 chr4 191154276 122728823 0.6420406886425077 5.158021353198436 chr5 180915260 138521866 0.7656726469618981 1.7636063819251169 chr6 171115067 150639193 0.8803385677311514 17.753435545267823 chr7 159138663 144442755 0.907653440572138 9.222446611211948 chr8 146364022 91235044 0.6233433787437188 2.4646747400559175 chr9 141213431 81578833 0.5776988238462955 15.26180745114465 chr10 135534747 81836667 0.6038058048686217 17.10277692893544 chr11 135006516 91100640 0.6747869858370391 7.020231505961304 chr12 133851895 70484371 0.52658478238205 1.3303363760273321 chr13 115169878 135939904 1.1803425197689277 2.251975266109326 chr14 107349540 37646495 0.35069079010492266 1.1329325685461868 chr15 102531392 45325122 0.44206092510672246 1.1552841272631178 chr16 90354753 69556060 0.769810748085383 12.59113727860596 chr17 81195210 47563113 0.5857871788249578 10.56435922073435 chr18 78077248 32911364 0.42152310491271416 12.410259074083747 chr19 59128983 24863776 0.4205006536303863 8.533362788187695 chr20 63025520 63091612 1.0010486545767492 2.520254942271637 chr21 48129895 16987922 0.3529598807560249 2.4737993409867247 chr22 51304566 11585638 0.22582079731460938 0.8207412693473731 chrMT 16571 2302385 138.94061915394363 104.48020385441177 chrX 155270560 103803575 0.6685335262524976 2.2323572640318687 chrY 59373566 20862056 0.3513694292844058 7.714904677365792