BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716254.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 = 3,609,939
number of mapped reads = 3,423,471 (94.83%)
number of supplementary alignments = 73,310 (2.03%)
number of secondary alignments = 0
number of mapped bases = 265,771,251 bp
number of sequenced bases = 265,673,317 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 268,672
duplication rate = 6%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.4301
>>>>>>> ACTG content
number of A's = 63,459,742 bp (23.89%)
number of C's = 54,492,672 bp (20.51%)
number of T's = 79,400,014 bp (29.89%)
number of G's = 68,310,432 bp (25.71%)
number of N's = 10,457 bp (0%)
GC percentage = 46.22%
>>>>>>> Mismatches and indels
general error rate = 0.0064
number of mismatches = 1,654,721
number of insertions = 19,985
mapped reads with insertion percentage = 0.57%
number of deletions = 46,975
mapped reads with deletion percentage = 1.35%
homopolymer indels = 40.25%
>>>>>>> Coverage
mean coverageData = 0.0859X
std coverageData = 0.615X
There is a 6.25% of reference with a coverageData >= 1X
There is a 1.44% of reference with a coverageData >= 2X
There is a 0.44% of reference with a coverageData >= 3X
There is a 0.16% of reference with a coverageData >= 4X
There is a 0.07% of reference with a coverageData >= 5X
There is a 0.04% of reference with a coverageData >= 6X
There is a 0.02% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% 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 29970618 0.12024290202269948 1.19325775030127
chr2 243199373 24400658 0.10033191162873599 0.6576740580713919
chr3 198022430 17032916 0.08601508425080936 0.38436678284778336
chr4 191154276 12447383 0.06511694773702054 0.5038487814197938
chr5 180915260 13196967 0.072945571313332 0.3602604925820653
chr6 171115067 15507558 0.0906264905357516 0.4318315956699359
chr7 159138663 16247765 0.10209816202867056 0.8343824371331058
chr8 146364022 15863023 0.10838061692510746 0.6540592092728955
chr9 141213431 8010479 0.05672604187345324 0.4351730909292158
chr10 135534747 13711207 0.10116377758096232 0.843101793821259
chr11 135006516 8209308 0.060806753949564925 0.46661353157393626
chr12 133851895 9532727 0.0712184687411411 0.352064144189061
chr13 115169878 4782290 0.04152379148999359 0.26164011701030654
chr14 107349540 5016556 0.046731043281601395 0.3194051556354457
chr15 102531392 5669623 0.05529645983934364 0.3029236058681909
chr16 90354753 8128156 0.0899582559868212 0.43386750562197307
chr17 81195210 8058050 0.09924292332023034 0.4762029317047855
chr18 78077248 7680047 0.09836472463783559 0.6683591634448012
chr19 59128983 8316557 0.14065110844203088 0.9274109755161236
chr20 63025520 7521217 0.11933605625149939 0.4940240895675623
chr21 48129895 4083317 0.08483951606376869 0.4879186323476879
chr22 51304566 5154689 0.1004723244320983 0.4438234522651052
chrMT 16571 159851 9.646430511133909 7.78332595317977
chrX 155270560 16226881 0.10450713258199107 0.45867935607355
chrY 59373566 843408 0.0142051093916104 0.44351859550675543