BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818868.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 = 2,377,369 number of mapped reads = 2,192,454 (92.22%) number of supplementary alignments = 33,932 (1.43%) number of secondary alignments = 0 number of mapped bases = 202,825,220 bp number of sequenced bases = 202,692,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 788,455 duplication rate = 30.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1634 >>>>>>> ACTG content number of A's = 58,311,242 bp (28.77%) number of C's = 43,030,988 bp (21.23%) number of T's = 58,353,154 bp (28.79%) number of G's = 42,994,183 bp (21.21%) number of N's = 2,831 bp (0%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,276,472 number of insertions = 29,859 mapped reads with insertion percentage = 1.31% number of deletions = 68,755 mapped reads with deletion percentage = 3.06% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0655X std coverageData = 0.8643X There is a 3.56% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 19504363 0.07825201366298702 1.3211741452665995 chr2 243199373 15523737 0.06383131999275343 1.3065461373405365 chr3 198022430 12503900 0.06314385698630201 0.4079883035581083 chr4 191154276 10158108 0.05314088814837707 0.485058883782983 chr5 180915260 8799775 0.04864031370266941 0.3818664818515927 chr6 171115067 10035683 0.058648739564237204 0.4420711092727484 chr7 159138663 18252853 0.11469779031636076 1.8677933800671427 chr8 146364022 17436413 0.1191304581668301 0.7117109449561859 chr9 141213431 7531630 0.05333508255316026 0.7227408425859765 chr10 135534747 9451098 0.06973191900376662 1.089300009879187 chr11 135006516 8934473 0.06617808728580182 0.5214832144003007 chr12 133851895 7888897 0.058937507011013926 0.40628987226320035 chr13 115169878 6136077 0.053278488321399455 0.37033278832198946 chr14 107349540 5846388 0.05446123010867117 0.4194233302288191 chr15 102531392 5675445 0.05535324244890775 0.3830517886683277 chr16 90354753 5160564 0.0571144718861663 0.895464027488704 chr17 81195210 5160236 0.06355345346110934 0.5289506392049996 chr18 78077248 3915849 0.05015352231677018 0.8070366517787482 chr19 59128983 3617033 0.061171912934812354 1.075481684436424 chr20 63025520 8187570 0.12990880519510192 0.6335289266314795 chr21 48129895 1976532 0.04106661774350432 0.38304246026277494 chr22 51304566 1844226 0.03594662510155529 0.3535257348274224 chrMT 16571 339012 20.45814977973568 12.341098787494229 chrX 155270560 8202167 0.052824997861796855 0.4432697699519042 chrY 59373566 743191 0.012517203362856798 0.9836521938740417