BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716382.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,654,455 number of mapped reads = 2,319,658 (87.39%) number of supplementary alignments = 9,154 (0.34%) number of secondary alignments = 0 number of mapped bases = 131,635,727 bp number of sequenced bases = 131,595,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,254 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1969 >>>>>>> ACTG content number of A's = 31,202,158 bp (23.71%) number of C's = 26,702,245 bp (20.29%) number of T's = 42,177,988 bp (32.05%) number of G's = 31,512,553 bp (23.95%) number of N's = 998 bp (0%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 702,485 number of insertions = 10,332 mapped reads with insertion percentage = 0.44% number of deletions = 25,247 mapped reads with deletion percentage = 1.08% homopolymer indels = 39.73% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.3295X There is a 3.73% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% 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 11136032 0.044678051173240606 0.42398496726426643 chr2 243199373 10363451 0.042612984039231055 0.49404429242118725 chr3 198022430 7515127 0.03795088768479409 0.22460340371996904 chr4 191154276 8059591 0.04216275549075345 0.26641596744621027 chr5 180915260 7443440 0.041143240210914214 0.22445612058901854 chr6 171115067 7027911 0.04107125762338626 0.2818439270094185 chr7 159138663 7524893 0.04728513397149755 0.48336254645342364 chr8 146364022 6754345 0.04614757716893022 0.31183617607637903 chr9 141213431 4390430 0.03109073952037891 0.24275214239133672 chr10 135534747 5936871 0.04380331340420033 0.4604218324366313 chr11 135006516 4711486 0.03489821187593642 0.26639701121605647 chr12 133851895 6586236 0.049205399744247175 0.24876805791788717 chr13 115169878 3971794 0.03448639582651985 0.20662371995024387 chr14 107349540 4423521 0.04120670661467203 0.24274221288330827 chr15 102531392 4902166 0.04781136688361746 0.25168084290437354 chr16 90354753 4631167 0.05125537778848225 0.2846601788956147 chr17 81195210 5989079 0.07376148174258063 0.32595929286930336 chr18 78077248 2454626 0.03143842877248952 0.3996569428050436 chr19 59128983 3461428 0.058540293175683406 0.4092326838686003 chr20 63025520 3869608 0.06139747835479977 0.2966533973516396 chr21 48129895 1647421 0.0342286431333374 0.23207784622410954 chr22 51304566 1238450 0.024139177008143876 0.17608783510795217 chrMT 16571 3379 0.2039104459598093 0.6356717764637199 chrX 155270560 7183688 0.04626561532334269 0.2642736070156508 chrY 59373566 409587 0.0068984739774599355 0.20005734203349748