BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695918.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 431,386,314 number of mapped reads = 427,950,443 (99.2%) number of supplementary alignments = 5,035,630 (1.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 214,892,073 number of mapped paired reads (second in pair) = 213,058,370 number of mapped paired reads (both in pair) = 425,446,176 number of mapped paired reads (singletons) = 2,504,267 number of mapped bases = 42,437,765,131 bp number of sequenced bases = 42,428,231,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,032,185 duplication rate = 13.34% >>>>>>> Insert size mean insert size = 77,964.1329 std insert size = 2,666,531.4929 median insert size = 325 >>>>>>> Mapping quality mean mapping quality = 53.8806 >>>>>>> ACTG content number of A's = 12,557,183,524 bp (29.6%) number of C's = 8,515,415,433 bp (20.07%) number of T's = 12,441,975,761 bp (29.32%) number of G's = 8,800,866,419 bp (20.74%) number of N's = 112,790,417 bp (0.27%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 329,278,019 number of insertions = 4,287,029 mapped reads with insertion percentage = 0.98% number of deletions = 4,135,182 mapped reads with deletion percentage = 0.95% homopolymer indels = 44.93% >>>>>>> Coverage mean coverageData = 13.7086X std coverageData = 16.8592X There is a 90.84% of reference with a coverageData >= 1X There is a 88.83% of reference with a coverageData >= 2X There is a 86.13% of reference with a coverageData >= 3X There is a 82.81% of reference with a coverageData >= 4X There is a 78.97% of reference with a coverageData >= 5X There is a 74.75% of reference with a coverageData >= 6X There is a 70.28% of reference with a coverageData >= 7X There is a 65.7% of reference with a coverageData >= 8X There is a 61.1% of reference with a coverageData >= 9X There is a 56.57% of reference with a coverageData >= 10X There is a 52.18% of reference with a coverageData >= 11X There is a 47.99% of reference with a coverageData >= 12X There is a 44.01% of reference with a coverageData >= 13X There is a 40.28% of reference with a coverageData >= 14X There is a 36.8% of reference with a coverageData >= 15X There is a 33.57% of reference with a coverageData >= 16X There is a 30.59% of reference with a coverageData >= 17X There is a 27.85% of reference with a coverageData >= 18X There is a 25.34% of reference with a coverageData >= 19X There is a 23.05% of reference with a coverageData >= 20X There is a 20.96% of reference with a coverageData >= 21X There is a 19.06% of reference with a coverageData >= 22X There is a 17.33% of reference with a coverageData >= 23X There is a 15.75% of reference with a coverageData >= 24X There is a 14.33% of reference with a coverageData >= 25X There is a 13.04% of reference with a coverageData >= 26X There is a 11.87% of reference with a coverageData >= 27X There is a 10.81% of reference with a coverageData >= 28X There is a 9.85% of reference with a coverageData >= 29X There is a 8.97% of reference with a coverageData >= 30X There is a 8.18% of reference with a coverageData >= 31X There is a 7.47% of reference with a coverageData >= 32X There is a 6.82% of reference with a coverageData >= 33X There is a 6.23% of reference with a coverageData >= 34X There is a 5.69% of reference with a coverageData >= 35X There is a 5.21% of reference with a coverageData >= 36X There is a 4.76% of reference with a coverageData >= 37X There is a 4.36% of reference with a coverageData >= 38X There is a 4% of reference with a coverageData >= 39X There is a 3.66% of reference with a coverageData >= 40X There is a 3.36% of reference with a coverageData >= 41X There is a 3.08% of reference with a coverageData >= 42X There is a 2.83% of reference with a coverageData >= 43X There is a 2.61% of reference with a coverageData >= 44X There is a 2.4% of reference with a coverageData >= 45X There is a 2.21% of reference with a coverageData >= 46X There is a 2.03% of reference with a coverageData >= 47X There is a 1.87% of reference with a coverageData >= 48X There is a 1.73% of reference with a coverageData >= 49X There is a 1.6% of reference with a coverageData >= 50X There is a 1.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3505480658 14.064079936635343 17.59465867009478 chr2 243199373 3766951210 15.489148526711045 19.51930101388762 chr3 198022430 3054358482 15.424305630427826 12.21908977572564 chr4 191154276 3082187885 16.12408547428989 16.668359285012997 chr5 180915260 2652805919 14.663251286817928 11.54051187519542 chr6 171115067 2792189847 16.31761536814289 14.903004440107518 chr7 159138663 2132990170 13.403343535693773 11.973975434625093 chr8 146364022 1941282664 13.263386981808958 11.386324801936238 chr9 141213431 1794707692 12.709185516496657 15.12194544222084 chr10 135534747 2021738331 14.91675290469978 18.71118174077877 chr11 135006516 2155837147 15.96839331073472 14.252514198563084 chr12 133851895 2075531859 15.506182105229067 12.738969436008821 chr13 115169878 1476474678 12.81997257998311 12.32149798188357 chr14 107349540 1277870649 11.903829760239308 12.356756377222824 chr15 102531392 1329943766 12.971088561832849 13.272730960311554 chr16 90354753 1053782170 11.662719835004141 19.76437866089225 chr17 81195210 975490989 12.014144541285132 14.943633942499646 chr18 78077248 1180140118 15.115032205028538 18.31747405733312 chr19 59128983 587827160 9.941438701896834 12.93237760173456 chr20 63025520 751930843 11.930577375640851 12.964093665657494 chr21 48129895 572955443 11.904356803604081 23.86448102715286 chr22 51304566 426472874 8.312571516539093 11.62004891187941 chrMT 16571 49640908 2995.649508176936 785.5626722025207 chrX 155270560 1511375497 9.733818806346806 9.043834082678572 chrY 59373566 267798172 4.510393935240474 18.91199074464556