BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819030.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,586,535 number of mapped reads = 1,399,424 (88.21%) number of supplementary alignments = 5,623 (0.35%) number of secondary alignments = 0 number of mapped bases = 79,947,194 bp number of sequenced bases = 79,926,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,588 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1158 >>>>>>> ACTG content number of A's = 20,879,207 bp (26.12%) number of C's = 14,879,568 bp (18.62%) number of T's = 24,369,136 bp (30.49%) number of G's = 19,796,897 bp (24.77%) number of N's = 1,778 bp (0%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 395,399 number of insertions = 4,906 mapped reads with insertion percentage = 0.35% number of deletions = 12,185 mapped reads with deletion percentage = 0.87% homopolymer indels = 39.79% >>>>>>> Coverage mean coverageData = 0.0258X std coverageData = 0.2084X There is a 2.35% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9037208 0.03625751447977335 0.3038013891658676 chr2 243199373 6618260 0.027213310290894542 0.2366559776117482 chr3 198022430 5290454 0.02671643813279132 0.1758071411911455 chr4 191154276 5076069 0.026554828415138357 0.18670725503969512 chr5 180915260 3956641 0.021870134116934083 0.16044445782974312 chr6 171115067 4207782 0.02459036526573081 0.17863720291243845 chr7 159138663 3427628 0.021538625092005454 0.1845324693318222 chr8 146364022 5095174 0.03481165610494087 0.22459201457013195 chr9 141213431 2882252 0.020410608109932546 0.2006761075276744 chr10 135534747 3751887 0.027682104279871493 0.2206184659931489 chr11 135006516 2531206 0.0187487691334839 0.18324880538368454 chr12 133851895 3630576 0.027123829662628236 0.17938235295730187 chr13 115169878 2499682 0.021704303620083718 0.15798486657345662 chr14 107349540 2820173 0.026270936978397857 0.18374598370095435 chr15 102531392 2277249 0.02221026122419171 0.16026701280416145 chr16 90354753 2384408 0.026389403111975747 0.18544827737144487 chr17 81195210 1783224 0.02196218225188407 0.16277059290901286 chr18 78077248 1933112 0.02475896691440764 0.3704374306858628 chr19 59128983 1555727 0.02631073495716982 0.2435230293315786 chr20 63025520 2493323 0.03956053040101851 0.21952187104009327 chr21 48129895 1029498 0.02138999056615436 0.1699350250665727 chr22 51304566 947426 0.018466699435679856 0.14510669387072508 chrMT 16571 6060 0.3656991129080924 0.6415248422421888 chrX 155270560 4486872 0.028897119969168657 0.20105847530705293 chrY 59373566 225303 0.0037946684893408627 0.08764415205413614