BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240207.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,587,498 number of mapped reads = 1,284,434 (80.91%) number of supplementary alignments = 4,480 (0.28%) number of secondary alignments = 0 number of mapped bases = 77,807,388 bp number of sequenced bases = 77,758,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,566 duplication rate = 7.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1649 >>>>>>> ACTG content number of A's = 20,625,493 bp (26.53%) number of C's = 13,126,799 bp (16.88%) number of T's = 25,698,418 bp (33.05%) number of G's = 18,289,430 bp (23.52%) number of N's = 18,132 bp (0.02%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 766,882 number of insertions = 5,477 mapped reads with insertion percentage = 0.42% number of deletions = 28,381 mapped reads with deletion percentage = 2.18% homopolymer indels = 51.05% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2642X There is a 1.91% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 5526386 0.022172004939558405 0.31276957800852473 chr2 243199373 9050815 0.03721561815046291 0.3151295462398807 chr3 198022430 5484431 0.02769600898241679 0.2156027369300317 chr4 191154276 5253865 0.027484946243106798 0.21862073335838064 chr5 180915260 4088912 0.02260125541648615 0.19311039959997772 chr6 171115067 4320488 0.025249021466940722 0.2333592355366944 chr7 159138663 4814811 0.030255444586712407 0.5445745222506245 chr8 146364022 4608728 0.03148812076235511 0.3122681559654407 chr9 141213431 2616388 0.018527897675682137 0.22034477825779664 chr10 135534747 3344846 0.024678881792578253 0.22279463446070324 chr11 135006516 3338531 0.024728665688995337 0.23794317971307363 chr12 133851895 3573086 0.02669432509715309 0.20817015310118017 chr13 115169878 1557954 0.013527443347643383 0.14788218454568355 chr14 107349540 2827947 0.02634335461521307 0.21213290528553186 chr15 102531392 2090176 0.02038571757613512 0.19171906760037974 chr16 90354753 2218881 0.024557435290648185 0.1998342611453008 chr17 81195210 2204569 0.027151466201023433 0.21878859347526888 chr18 78077248 1656936 0.021221752078147017 0.31415568337161803 chr19 59128983 1416952 0.023963747186384044 0.2595830425659729 chr20 63025520 1549036 0.024577917008856094 0.20098774714260112 chr21 48129895 1283277 0.0266627841178544 0.21094758465522964 chr22 51304566 695144 0.013549359329927867 0.14465099540698043 chrMT 16571 66699 4.025043751131495 5.045134584516274 chrX 155270560 4062706 0.02616533359575698 0.2208278790500534 chrY 59373566 155824 0.002624467595562645 0.06401980297421123