BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008766.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 = 2,455,931 number of mapped reads = 2,277,348 (92.73%) number of supplementary alignments = 17,912 (0.73%) number of secondary alignments = 0 number of mapped bases = 147,541,817 bp number of sequenced bases = 147,480,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,893 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2205 >>>>>>> ACTG content number of A's = 39,448,788 bp (26.75%) number of C's = 26,094,365 bp (17.69%) number of T's = 47,558,020 bp (32.25%) number of G's = 34,350,762 bp (23.29%) number of N's = 28,095 bp (0.02%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,023,076 number of insertions = 11,409 mapped reads with insertion percentage = 0.5% number of deletions = 38,137 mapped reads with deletion percentage = 1.66% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.4281X There is a 4.03% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 13176762 0.052865513221730345 0.8526452465496352 chr2 243199373 8426279 0.03464761810878517 0.4703769731298318 chr3 198022430 9416879 0.0475546078290222 0.24894846495503398 chr4 191154276 7817028 0.040893817096720346 0.24115993553776888 chr5 180915260 7569773 0.04184153951413496 0.23570493145528862 chr6 171115067 7820622 0.04570387714601427 0.30089694503790476 chr7 159138663 8550049 0.05372703803600511 0.5283584115454777 chr8 146364022 15833448 0.10817855224011266 0.516381178615333 chr9 141213431 3094091 0.021910741620604062 0.36161361730207076 chr10 135534747 8393853 0.061931373214575 0.3933290423851786 chr11 135006516 5552059 0.04112437802631689 0.3657507063612394 chr12 133851895 8603819 0.06427864917414879 0.2935503824644529 chr13 115169878 4146964 0.03600736644003391 0.21408080963651693 chr14 107349540 4501742 0.041935363672727426 0.2443792454668358 chr15 102531392 4731634 0.04614814943700365 0.25248470285039126 chr16 90354753 4051558 0.04484056306368299 0.2797820423190196 chr17 81195210 5693972 0.0701269446806037 0.3868806306876314 chr18 78077248 1094556 0.014018885501702109 0.7406924182849193 chr19 59128983 2688557 0.04546935975543499 0.5741588758774104 chr20 63025520 2691110 0.04269873536941861 0.2527557682103033 chr21 48129895 1613167 0.033516944094725325 0.22147448554831003 chr22 51304566 1861361 0.03628061096940183 0.21200746804908308 chrMT 16571 70034 4.226298956007483 3.23583352160466 chrX 155270560 9733185 0.06268532167334233 0.3381727515261334 chrY 59373566 409315 0.00689389281418603 0.23411686282939806