BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927038.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 = 23,242,730 number of mapped reads = 22,499,318 (96.8%) number of supplementary alignments = 931,783 (4.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,308,871 number of mapped paired reads (second in pair) = 11,190,447 number of mapped paired reads (both in pair) = 22,057,582 number of mapped paired reads (singletons) = 441,736 number of mapped bases = 2,010,173,493 bp number of sequenced bases = 2,008,628,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,119,239 duplication rate = 7.39% >>>>>>> Insert size mean insert size = 446,431.4259 std insert size = 6,510,384.155 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 52.3267 >>>>>>> ACTG content number of A's = 576,757,246 bp (28.71%) number of C's = 382,095,675 bp (19.02%) number of T's = 593,056,198 bp (29.53%) number of G's = 456,511,130 bp (22.73%) number of N's = 208,688 bp (0.01%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 21,891,605 number of insertions = 352,996 mapped reads with insertion percentage = 1.54% number of deletions = 1,054,710 mapped reads with deletion percentage = 4.57% homopolymer indels = 51.69% >>>>>>> Coverage mean coverageData = 0.6493X std coverageData = 2.489X There is a 29.89% of reference with a coverageData >= 1X There is a 14.81% of reference with a coverageData >= 2X There is a 7.66% of reference with a coverageData >= 3X There is a 4.32% of reference with a coverageData >= 4X There is a 2.55% of reference with a coverageData >= 5X There is a 1.57% of reference with a coverageData >= 6X There is a 1% of reference with a coverageData >= 7X There is a 0.65% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 159619531 0.6403977264313415 2.677968000549151 chr2 243199373 185880268 0.7643122829926046 4.436746589910242 chr3 198022430 140251382 0.7082600794263559 1.5025451190199837 chr4 191154276 125159218 0.6547550000921769 2.0873439805471423 chr5 180915260 122818678 0.6788740651286133 1.433213607103615 chr6 171115067 119577128 0.6988112157300561 1.4941111265094793 chr7 159138663 102047348 0.6412479913822073 1.7769949207561162 chr8 146364022 107768850 0.7363069730346711 1.7734543697952425 chr9 141213431 86144295 0.6100290488657556 2.691058221778392 chr10 135534747 99709376 0.7356739006566339 5.128879022348694 chr11 135006516 92682921 0.6865070201500496 2.078963474320095 chr12 133851895 89943372 0.6719618874278919 1.453825171102732 chr13 115169878 62193159 0.5400123719849733 1.2756471435608303 chr14 107349540 58111850 0.5413330136300537 1.3728024480192598 chr15 102531392 54311697 0.5297079844580672 1.283635427181335 chr16 90354753 60748753 0.6723359976425368 3.500231435220157 chr17 81195210 49063434 0.6042651284478481 1.8147505531015624 chr18 78077248 51700797 0.66217493987493 2.733024228497817 chr19 59128983 30216245 0.5110225724667038 1.7792334918132142 chr20 63025520 44094469 0.6996288011586418 1.5832052641765728 chr21 48129895 24237303 0.503581048743198 1.791938880800103 chr22 51304566 23653808 0.46104683937877966 1.319614845533086 chrMT 16571 52142 3.1465813771045803 3.0992325499471756 chrX 155270560 116300140 0.7490160401302088 1.6958257876557357 chrY 59373566 3887329 0.06547238547201291 3.0817066328065197