BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926966.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 32,527,614 number of mapped reads = 31,932,464 (98.17%) number of supplementary alignments = 506,111 (1.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,981,160 number of mapped paired reads (second in pair) = 15,951,304 number of mapped paired reads (both in pair) = 31,611,234 number of mapped paired reads (singletons) = 321,230 number of mapped bases = 3,003,097,806 bp number of sequenced bases = 3,000,848,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,579,980 duplication rate = 6.37% >>>>>>> Insert size mean insert size = 146,960.6557 std insert size = 3,787,975.3198 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.2989 >>>>>>> ACTG content number of A's = 849,502,786 bp (28.31%) number of C's = 609,064,704 bp (20.3%) number of T's = 862,316,714 bp (28.74%) number of G's = 679,615,618 bp (22.65%) number of N's = 348,382 bp (0.01%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 28,844,664 number of insertions = 488,887 mapped reads with insertion percentage = 1.51% number of deletions = 1,567,595 mapped reads with deletion percentage = 4.78% homopolymer indels = 52.55% >>>>>>> Coverage mean coverageData = 0.9701X std coverageData = 3.7712X There is a 35.28% of reference with a coverageData >= 1X There is a 20.96% of reference with a coverageData >= 2X There is a 12.73% of reference with a coverageData >= 3X There is a 8.21% of reference with a coverageData >= 4X There is a 5.43% of reference with a coverageData >= 5X There is a 3.68% of reference with a coverageData >= 6X There is a 2.55% of reference with a coverageData >= 7X There is a 1.79% of reference with a coverageData >= 8X There is a 1.27% of reference with a coverageData >= 9X There is a 0.91% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.21% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% 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 245987451 0.9869080767505891 4.52259841616578 chr2 243199373 260243569 1.0700832234464683 6.758617216114938 chr3 198022430 204408136 1.0322473873287992 2.0205644252516866 chr4 191154276 176519299 0.9234389242749662 3.0250022198671327 chr5 180915260 182963009 1.0113188296001123 1.9743956543815804 chr6 171115067 174105940 1.0174787238344125 3.4708082332558634 chr7 159138663 151899011 0.954507271435352 2.8295772562457513 chr8 146364022 155352405 1.0614111506173287 2.4875517359084114 chr9 141213431 128491713 0.9099114162873077 4.376665419619635 chr10 135534747 145481193 1.0733866865889379 5.261325742887212 chr11 135006516 144473071 1.0701192452073942 3.294447243305566 chr12 133851895 135986109 1.01594459308925 2.1101431093040732 chr13 115169878 91481129 0.7943147165615648 1.7699874315942636 chr14 107349540 89296440 0.8318288089543746 1.8875740530633072 chr15 102531392 90227235 0.8799961966770138 1.958670005728943 chr16 90354753 97975867 1.0843465755476085 7.413072463281904 chr17 81195210 80088197 0.9863660307055059 3.6210600404531843 chr18 78077248 81770723 1.0473053942679946 4.746740266504645 chr19 59128983 49525591 0.8375857064884745 3.151308419692428 chr20 63025520 71283624 1.1310279391586138 2.3534174487621695 chr21 48129895 36359301 0.7554411037048803 2.7886628386679675 chr22 51304566 37992926 0.7405369338861574 1.9085726168410357 chrMT 16571 32097 1.936938024259248 2.3619216946909884 chrX 155270560 166049384 1.0694196246860963 2.3490760281449536 chrY 59373566 5104386 0.0859706826435185 2.735088524103088