BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617410.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 27,925,550 (87.27%) number of supplementary alignments = 388,408 (1.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,291,846 number of mapped paired reads (second in pair) = 13,633,704 number of mapped paired reads (both in pair) = 26,906,080 number of mapped paired reads (singletons) = 1,019,470 number of mapped bases = 2,731,093,256 bp number of sequenced bases = 2,730,515,567 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,178,656 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 48,556.3252 std insert size = 2,099,312.7541 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 53.6874 >>>>>>> ACTG content number of A's = 817,580,436 bp (29.94%) number of C's = 546,500,650 bp (20.01%) number of T's = 806,627,909 bp (29.54%) number of G's = 558,096,006 bp (20.44%) number of N's = 1,710,566 bp (0.06%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0161 number of mismatches = 43,445,523 number of insertions = 222,170 mapped reads with insertion percentage = 0.78% number of deletions = 260,304 mapped reads with deletion percentage = 0.91% homopolymer indels = 43.96% >>>>>>> Coverage mean coverageData = 0.8822X std coverageData = 2.6965X There is a 28.6% of reference with a coverageData >= 1X There is a 16.08% of reference with a coverageData >= 2X There is a 10.13% of reference with a coverageData >= 3X There is a 6.91% of reference with a coverageData >= 4X There is a 4.97% of reference with a coverageData >= 5X There is a 3.7% of reference with a coverageData >= 6X There is a 2.84% of reference with a coverageData >= 7X There is a 2.23% of reference with a coverageData >= 8X There is a 1.78% of reference with a coverageData >= 9X There is a 1.45% of reference with a coverageData >= 10X There is a 1.19% of reference with a coverageData >= 11X There is a 0.99% of reference with a coverageData >= 12X There is a 0.84% of reference with a coverageData >= 13X There is a 0.71% of reference with a coverageData >= 14X There is a 0.61% of reference with a coverageData >= 15X There is a 0.52% of reference with a coverageData >= 16X There is a 0.45% of reference with a coverageData >= 17X There is a 0.4% of reference with a coverageData >= 18X There is a 0.35% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.17% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175195906 0.7028905496688813 2.5260516122469 chr2 243199373 273090976 1.1229098686862158 2.84462560692218 chr3 198022430 231014660 1.166608550354624 3.1517747781014314 chr4 191154276 132669077 0.6940419004804266 2.130516502356321 chr5 180915260 175389887 0.9694587786569248 2.6682783359931777 chr6 171115067 125829582 0.7353506865646144 2.4184667881773168 chr7 159138663 204471268 1.2848622964741132 2.999663776281008 chr8 146364022 120867385 0.8257998335137305 2.9901271982225928 chr9 141213431 108984011 0.7717680267962613 2.4003401484125564 chr10 135534747 87552953 0.6459816020463004 2.2124604322143266 chr11 135006516 202140692 1.4972661912110967 3.539526037734811 chr12 133851895 130260524 0.9731690686934241 2.5746080542691434 chr13 115169878 119208934 1.0350704200624403 2.5852056885073855 chr14 107349540 78980296 0.7357301763938625 2.6489794875408466 chr15 102531392 62489297 0.6094650212102846 2.171670214301599 chr16 90354753 67950750 0.7520440014926497 3.0269179330792593 chr17 81195210 83313876 1.0260934850713483 3.34949742932094 chr18 78077248 39449474 0.5052620963279854 1.8553315837872582 chr19 59128983 38198522 0.6460202773993254 2.120419116175481 chr20 63025520 91993291 1.4596197064300303 4.294390380500171 chr21 48129895 37524879 0.7796584430529092 2.3504902301455237 chr22 51304566 21599191 0.42099939019072885 1.8825237654577887 chrMT 16571 166303 10.035785408243317 4.913213080407404 chrX 155270560 120537504 0.7763062360308355 2.3771458724670285 chrY 59373566 2214018 0.03728962481384392 0.5263705427911046