BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038484.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 = 19,380,598 number of mapped reads = 18,666,711 (96.32%) number of supplementary alignments = 169,627 (0.88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,418,019 number of mapped paired reads (second in pair) = 9,248,692 number of mapped paired reads (both in pair) = 18,473,848 number of mapped paired reads (singletons) = 192,863 number of mapped bases = 2,738,808,327 bp number of sequenced bases = 2,737,796,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,172,025 duplication rate = 8.27% >>>>>>> Insert size mean insert size = 81,612.3116 std insert size = 2,828,171.0225 median insert size = 272 >>>>>>> Mapping quality mean mapping quality = 54.2548 >>>>>>> ACTG content number of A's = 789,430,633 bp (28.83%) number of C's = 582,620,318 bp (21.28%) number of T's = 784,374,849 bp (28.65%) number of G's = 581,121,786 bp (21.23%) number of N's = 248,911 bp (0.01%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 28,257,366 number of insertions = 348,045 mapped reads with insertion percentage = 1.75% number of deletions = 368,071 mapped reads with deletion percentage = 1.88% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 0.8847X std coverageData = 11.6903X There is a 47.24% of reference with a coverageData >= 1X There is a 22.31% of reference with a coverageData >= 2X There is a 8.83% of reference with a coverageData >= 3X There is a 3.63% of reference with a coverageData >= 4X There is a 1.38% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% 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 0.01% 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 225845693 0.9060988177036478 29.85236132612974 chr2 243199373 232288097 0.9551344402520314 8.366335835990512 chr3 198022430 176651506 0.8920782660832917 1.3526139107291866 chr4 191154276 174926662 0.9151072403946643 7.370247154101406 chr5 180915260 160208802 0.8855460948954775 1.2680289305927854 chr6 171115067 153820666 0.8989311619180794 4.544782765455281 chr7 159138663 147457505 0.9265976112919838 9.165732322870408 chr8 146364022 135722522 0.9272942909426197 7.580821655541191 chr9 141213431 115591203 0.8185567207130602 13.004857482978265 chr10 135534747 147331176 1.087036197440941 25.529486330758616 chr11 135006516 124395147 0.9214010603754859 4.408297524911587 chr12 133851895 119156814 0.8902138740732808 1.4753165385909779 chr13 115169878 83837356 0.7279451663567795 1.1221525812767603 chr14 107349540 80974208 0.7543041917086929 1.231352159340739 chr15 102531392 77176054 0.752706585705966 1.1498721723871839 chr16 90354753 89232143 0.9875755290925315 7.240512175642857 chr17 81195210 80173314 0.9874143314611785 6.046183088637916 chr18 78077248 74253375 0.9510244905148296 10.581533424694603 chr19 59128983 58786227 0.994203248853443 12.53225721279326 chr20 63025520 59038004 0.936731723911203 2.563061830977854 chr21 48129895 37976131 0.7890341543441971 4.013847292395951 chr22 51304566 35034303 0.68286910369732 1.1680046058108986 chrMT 16571 1272388 76.78402027638646 13.304230105763823 chrX 155270560 138773686 0.8937540123510858 2.6434806853947967 chrY 59373566 8885345 0.14965153011021773 7.959443536923355