BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6008717.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 = 2,028,909
number of mapped reads = 1,623,130 (80%)
number of supplementary alignments = 7,683 (0.38%)
number of secondary alignments = 0
number of mapped bases = 108,828,556 bp
number of sequenced bases = 108,779,587 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 44,789
duplication rate = 2.18%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.3744
>>>>>>> ACTG content
number of A's = 33,214,463 bp (30.53%)
number of C's = 19,001,434 bp (17.47%)
number of T's = 32,667,922 bp (30.03%)
number of G's = 23,880,285 bp (21.95%)
number of N's = 15,483 bp (0.01%)
GC percentage = 39.42%
>>>>>>> Mismatches and indels
general error rate = 0.0089
number of mismatches = 949,556
number of insertions = 8,532
mapped reads with insertion percentage = 0.52%
number of deletions = 30,195
mapped reads with deletion percentage = 1.84%
homopolymer indels = 48.21%
>>>>>>> Coverage
mean coverageData = 0.0352X
std coverageData = 0.2714X
There is a 3.1% of reference with a coverageData >= 1X
There is a 0.31% of reference with a coverageData >= 2X
There is a 0.05% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0% 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 8919442 0.03578503421261285 0.3877386269902273
chr2 243199373 9502049 0.03907102589446232 0.3285548838856719
chr3 198022430 8740666 0.04413977749894292 0.23601340394252796
chr4 191154276 6159820 0.03222433800016067 0.20197541957497042
chr5 180915260 5202297 0.028755435003105873 0.18597393529044687
chr6 171115067 5905908 0.03451424882415527 0.23254558225480404
chr7 159138663 6260473 0.03933973606401356 0.3302279993607066
chr8 146364022 9298718 0.06353144627304652 0.4014824542001436
chr9 141213431 3572731 0.025300220911706337 0.2362438741618428
chr10 135534747 5981140 0.044129938133134226 0.3151527280867684
chr11 135006516 4881551 0.03615789181612538 0.27074806883211316
chr12 133851895 4857120 0.036287271091679354 0.2110323929614265
chr13 115169878 3040067 0.0263963724959403 0.178486174272153
chr14 107349540 3909501 0.03641842340451575 0.2174184605282952
chr15 102531392 2791287 0.027223730659971922 0.18250204993771407
chr16 90354753 2550518 0.02822782327787449 0.20499316225199762
chr17 81195210 2904974 0.03577765240092365 0.24638900655676413
chr18 78077248 1854870 0.023756856799051113 0.3897520693330522
chr19 59128983 1853138 0.03134060330447422 0.2510941015299263
chr20 63025520 2354478 0.0373575339005533 0.21510179853573114
chr21 48129895 1090024 0.022647545771708 0.17529117716127948
chr22 51304566 1171893 0.022841885067305705 0.1653235001892976
chrMT 16571 32485 1.960352422907489 2.3670380629865035
chrX 155270560 5750235 0.0370336463010116 0.23380382890593335
chrY 59373566 243171 0.004095610494407562 0.10467418422014899