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
A3 F50 I1 R1 300 54.7 1718999 98.4% 1691495 149.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,511,541 (G)5→6 coding (874/957 nt) fecD ← ferric citrate ABC transporter permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,511,5361.G92.9% 132.3 / 3.7 42coding (879/957 nt)fecDferric citrate ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base . (3/0);  new base G (20/19);  total (23/19)
Fisher's exact test for biased strand distribution p-value = 2.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGTGAAACGTCGTTAAGTACCTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑T‑GGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACGAGACCAATAAAGCTA  >  NC_000913/4511389‑4511677
                                                                                                                                                       |                                                                                                                                             
gagTGAAACGTCGTTAAGTACCTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑T‑ggg                                                                                                                                            <  2:52626/151‑1 (MQ=255)
     aaaCGTCGTTAAGTACCTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑g‑gggggg                                                                                                                                         >  2:92800/1‑148 (MQ=255)
       aCGTCGTTAAGTACCTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACTCCAACCGGGAGCTCC‑C‑G‑T‑ggggggatg                                                                                                                                      >  2:177609/1‑146 (MQ=255)
           cgtTAAGTACCTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGaataa                                                                                                                                  <  2:717645/151‑1 (MQ=255)
            gtTAAGTACCTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑C‑G‑TGGGGGGATGaataa                                                                                                                                  >  1:776419/1‑150 (MQ=255)
                 gTACCTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCg                                                                                                                            <  1:499405/151‑1 (MQ=255)
                    ccTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCca                                                                                                                         <  2:635926/151‑1 (MQ=255)
                        gtctgtcCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑AGG‑G‑GGGGGATGAATAATTCTCGCcagc                                                                                                                       >  1:146535/1‑149 (MQ=255)
                            gtcCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCCACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCcagc                                                                                                                       >  2:405233/1‑145 (MQ=255)
                               ccGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCa                                                                                                              <  2:507483/151‑1 (MQ=255)
                                 gTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCaa                                                                                                             >  2:574829/1‑150 (MQ=255)
                                       gACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑C‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGAACGGCAAccacca                                                                                                       >  2:804385/1‑150 (MQ=255)
                                       gACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAAccacca                                                                                                       <  2:634660/150‑1 (MQ=255)
                                             cAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCaa                                                                                                <  2:59100/151‑1 (MQ=255)
                                              aGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCGCGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAAc                                                                                               <  2:448395/151‑1 (MQ=255)
                                              aGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAAc                                                                                               <  2:23217/151‑1 (MQ=255)
                                                    tCAGTTCGGAAAGTGATTTATCGCATTCTCACACGCAACCAGACAAACCACGGCGCACCGATACTGGCGCTTAGCCCCCCAACCGGGGGCACC‑A‑GAG‑GGGGGGAGAACAATTCTAGGCAAGAGATCGGCAACCACCAACAGCAACGccc                                                                                           >  1:91446/1‑147 (MQ=255)
                                                     cAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCt                                                                                         <  1:371165/150‑1 (MQ=255)
                                                       gTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTc                                                                                      <  2:146558/151‑1 (MQ=255)
                                                       gTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTc                                                                                      >  1:287863/1‑151 (MQ=255)
                                                            tAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGGGCCCC‑A‑G‑TGGGGGGAAGAATAATTCTCGCCAGCAGAACGGCAACCCCCAACAGCAACGCACCTGTCAggg                                                                                  >  1:848289/1‑150 (MQ=255)
                                                             aaaGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGc                                                                                 <  1:766655/150‑1 (MQ=255)
                                                               aGTCATTTATCGCATTCTCACAAGCTACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGa                                                                              <  1:98434/151‑1 (MQ=255)
                                                               aGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGa                                                                              <  1:734053/151‑1 (MQ=255)
                                                                   aTTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCCACCGGGAGCTCC‑C‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCCACCACCAACAGCAACGCACCTGTCAGGGCCGAAAc                                                                           >  1:200914/1‑150 (MQ=255)
                                                                   aTTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAAc                                                                           >  2:597712/1‑150 (MQ=255)
                                                                         cGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGG‑CGAAACAGggagc                                                                    >  2:216321/1‑150 (MQ=255)
                                                                            aTTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGcagcag                                                                  >  2:768735/1‑150 (MQ=255)
                                                                                 cacaAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCt                                                               <  2:287888/148‑1 (MQ=255)
                                                                                       cAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAAACGGGAGCTCCAA‑C‑G‑GGGGGGTGAATAATTGTCGCCAGCAGATTAGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCCGTCCGCGGTGACg                                                      >  2:86454/1‑151 (MQ=255)
                                                                                         aCCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTc                                                    <  2:703278/151‑1 (MQ=255)
                                                                                            aGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCAc                                                 >  2:588479/1‑151 (MQ=255)
                                                                                            aGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCAc                                                 >  2:413585/1‑151 (MQ=255)
                                                                                                aaaCCACGGCGCACCGATAATGGCGGTCAGCACGCCCACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGGCCACCGGt                                             >  1:82359/1‑151 (MQ=255)
                                                                                                aaaCCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGt                                             <  1:323933/151‑1 (MQ=255)
                                                                                                aaaCCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGGCTGCGGTGACGTCCACCgg                                              >  1:843819/1‑150 (MQ=255)
                                                                                                    cACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATg                                         >  2:718638/1‑151 (MQ=255)
                                                                                                                        ggTCAGCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGcac                     <  2:646283/151‑1 (MQ=255)
                                                                                                                             gCACGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACga                <  2:240743/151‑1 (MQ=255)
                                                                                                                               aCGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACgaga              <  2:85994/151‑1 (MQ=255)
                                                                                                                               aCGCCAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACg                 >  2:520845/1‑148 (MQ=255)
                                                                                                                                   cAACCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACGAGACCa           >  1:287885/1‑150 (MQ=255)
                                                                                                                                     aCCGGGAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACGAGACCAAt         >  2:6119/1‑150 (MQ=255)
                                                                                                                                         ggAGCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACGAGACCAATAAAGc    >  2:786513/1‑151 (MQ=255)
                                                                                                                                            gCTCC‑A‑G‑TGGGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACGAGACCAATAAAGCTa  >  1:585936/1‑150 (MQ=255)
                                                                                                                                                       |                                                                                                                                             
GAGTGAAACGTCGTTAAGTACCTTGTCTGTCCCGTAACTGACCGTCAGATTTTCAGTTCGTAAAGTCATTTATCGCATTCTCACAAGCAACCAGACAAACCACGGCGCACCGATAATGGCGGTCAGCACGCCAACCGGGAGCTCC‑A‑G‑T‑GGGGGATGAATAATTCTCGCCAGCAGATCGGCAACCACCAACAGCAACGCACCTGTCAGGGCCGAAACAGGCAGCAGTCTGCGGTGACGTCCACCGGTGATGCTACGCATCATATGCGGCACCACGAGACCAATAAAGCTA  >  NC_000913/4511389‑4511677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A