Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F13 I0 R1 213 60.4 2554362 98.6% 2518600 147.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947_CJ‑RC 4,442,726 A→C 24.1% intergenic (‑89/+49) nicP‑II ← / ← nicT porin‑like protein/metabolite transport protein NicT

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC4,442,7260AC24.1% 36.1 / 2.9 28intergenic (‑89/+49)nicP‑II/nicTporin‑like protein/metabolite transport protein NicT
Reads supporting (aligned to +/- strand):  ref base A (10/9);  new base C (2/4);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 6.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCGGT  >  NC_002947_CJ‑RC/4442583‑4442873
                                                                                                                                               |                                                                                                                                                   
aaCCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCgg                                                                                                                                                <  3:103849/149‑1 (MQ=255)
     ccgGCCAGGCGTGCAGACGAAGAAAAACGCGGCCCAGTGAAACCTTGCATAGGGCTACACCTGGATTTGGGCAACAGCAACCCGGCGCGCCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGACACGTCGGCAGCCCGGcccc                                                                                                                                           >  6:177714/1‑149 (MQ=255)
      cgGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCg                                                                                                                                          <  4:142413/149‑1 (MQ=255)
       ggCCAGGCTTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCgg                                                                                                                                         <  3:27133/149‑1 (MQ=255)
        gCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCCGc                                                                                                                                        >  8:293782/1‑149 (MQ=255)
            ggCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCccgcccgc                                                                                                                                    >  6:115601/1‑149 (MQ=255)
               gTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGcctg                                                                                                                                 <  5:185899/149‑1 (MQ=255)
                       gaagaaAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGGCGGCGGGCCCCCGCCCCccagcccgggcc                                                                                                                         >  3:290440/1‑144 (MQ=255)
                         ataaaacCGGGGCGCTGTGAAACCTTGATTTGGGCTACTCCTGGATTTGGGCAACAGAAACCGGGCGCGGCGGCACTGCTTGGCCACCGGGGTGGGGGTTGAATCGAGAGAGGTCGGCCGGCGGGCCCCGGCCCGCCTGCCCTGCCGtt                                                                                                                       <  6:284184/147‑1 (MQ=255)
                                 gcggcgCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGGGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAg                                                                                                               <  6:225684/149‑1 (MQ=255)
                                            aaaCCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGTAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCg                                                                                                     >  7:106700/1‑148 (MQ=255)
                                                    cATAGGGCTACTCTTGTTTTTGGCAAACAGCACCCCGGCGGGGGGGAACTCCTGGGCCACGGGGGGGGGGTTTGATTCTAGAGTGGGGGGCCGGGGGGCCCGGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGtt                                                                                            <  4:130401/149‑1 (MQ=255)
                                                                 cTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCGGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGcc                                                                               >  6:103312/1‑149 (MQ=255)
                                                                 cTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCCGGCCCCCGCCCCCCAGCCCAGCCCTTTCGGGAAACCCAAGGCCCCAAGCCGTTTACCAACATGGcc                                                                               >  2:293224/1‑149 (MQ=255)
                                                                 cTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCAGGGCCCCCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGc                                                                                <  5:57000/148‑1 (MQ=255)
                                                                    gATTTGGGCACCACCACCCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCAGCGAGAGAGGTCGGCCGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGc                                                                            <  8:229743/149‑1 (MQ=255)
                                                                    gATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCCCCTGCCCAGCCGTTGCGTGAAGCGCGGGGCCGCGAGCCGTTGACCAGCTTGGCCGGc                                                                            >  6:130922/1‑149 (MQ=255)
                                                                     aTTTGGGCAACAGCAACCCGGGGCGGCGGCAGTGGAGGGCCACCGGCGTGCGGGTTGCTTCGAGTGAGGTCGGCTGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCa                                                                           <  5:115601/149‑1 (MQ=255)
                                                                        tGGGCAACCGCACCCCGGCGCGGCGGCACTGCATGCCCACCGGCGTGCGGGTTGAATCGAGCGTGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAg                                                                         <  8:121234/148‑1 (MQ=255)
                                                                                 gCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCCCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCa                                                               >  2:200538/1‑149 (MQ=255)
                                                                                         gcggggcgGCCGTGCTGGGCCCCGGGGGGGGGGGTTGCTTGGCGCGGGGGCGGCGGGCGGGCCCCGGCCGGCGTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAagcag                                                       <  7:293782/149‑1 (MQ=255)
                                                                                                        aTGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCGGCCCGCCGGCCCAGCCGGTGGGGGTAGCGCTGGGGCGCGAGCGGGTGGCCCGCTTGGGCGGCGAGGCGATGACCCGGGAGCAGCTGAGGGTCAGGccg                                        >  2:33509/1‑147 (MQ=255)
                                                                                                                       cGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCca                          <  6:62387/148‑1 (MQ=255)
                                                                                                                                 cgtgagagGGCGGCTGGCGGGCCGCGGCCGGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGt               <  7:136363/146‑1 (MQ=255)
                                                                                                                                            ggCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCg    >  4:131470/1‑149 (MQ=255)
                                                                                                                                             gCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAg          <  4:308152/142‑1 (MQ=255)
                                                                                                                                             gCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAg          >  3:308152/1‑142 (MQ=255)
                                                                                                                                              cAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCGGt  <  1:225551/149‑1 (MQ=255)
                                                                                                                                               aGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCGGt  >  8:116838/1‑148 (MQ=255)
                                                                                                                                               |                                                                                                                                                   
AACCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCGGT  >  NC_002947_CJ‑RC/4442583‑4442873

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A