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 1,260,849 G→A intergenic (‑46/+79) dauA ← / ← prs C4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,260,8490GA97.9% 146.7 / ‑6.8 48intergenic (‑46/+79)dauA/prsC4‑dicarboxylic acid transporter/phosphoribosylpyrophosphate synthase
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (25/22);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 4.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCAGGTCACGGGTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAGGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGCTTCGGCCAGCATAC  >  NC_000913/1260703‑1260995
                                                                                                                                                  |                                                                                                                                                  
aTCAGGTCACGGGTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTg                                                                                                                                                 >  1:500169/1‑150 (MQ=255)
 tCAGGTCACGGGTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGa                                                                                                                                                >  1:68925/1‑150 (MQ=255)
   aGGTCACGGGTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAagg                                                                                                                                             <  1:53333/151‑1 (MQ=255)
     gTCACGGGTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATTAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAaggag                                                                                                                                           <  1:756910/151‑1 (MQ=255)
       cACGGGTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAaggagg                                                                                                                                          <  2:174870/150‑1 (MQ=255)
          gggTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATa                                                                                                                                      <  2:347586/151‑1 (MQ=255)
           ggTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAg                                                                                                                                     <  1:314077/151‑1 (MQ=255)
              aaaCCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGt                                                                                                                                   <  2:414666/150‑1 (MQ=255)
                     gCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACaa                                                                                                                            <  1:829971/150‑1 (MQ=255)
                      cGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAAt                                                                                                                          >  2:859131/1‑151 (MQ=255)
                                 ttttCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTAc                                                                                                                 >  1:298203/1‑149 (MQ=255)
                                    tctttcCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGAc                                                                                                             >  1:793125/1‑150 (MQ=255)
                                              aaGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACccg                                                                                                  >  1:346720/1‑151 (MQ=255)
                                               aGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACccgc                                                                                                 >  2:116270/1‑151 (MQ=255)
                                               aGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACccgc                                                                                                 <  2:583306/151‑1 (MQ=255)
                                                gCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATCCAAATGGATATTACAGACAAAAAAACccgcc                                                                                                <  1:52332/151‑1 (MQ=255)
                                                 cGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTAATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACccgccg                                                                                               >  2:708087/1‑151 (MQ=255)
                                                                ggAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGAATCACCTGCCAACAAAATGGCAAGTGAAGGAGGCATGGGTCATAAAAATGGATATAACAGAAAAAAAACCCCGCCGCAGCGGGTCTTTGa                                                                                 <  1:859072/150‑1 (MQ=255)
                                                                ggAAAGGCATCACAGGTGAGAAAAATTTTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAAGGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAACCCCGCCGCAGCGGGTCTTTGAg                                                                                <  2:448355/151‑1 (MQ=255)
                                                                         tCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCg                                                                       >  1:107714/1‑151 (MQ=255)
                                                                          cacaTGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCg                                                                       >  2:776673/1‑150 (MQ=255)
                                                                               gtgAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAgt                                                                 >  1:693581/1‑151 (MQ=255)
                                                                                 gAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAgtgt                                                               >  1:21563/1‑151 (MQ=255)
                                                                                  aGGAAAATATTTTGTTCACAATAATTTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAACCCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAgtgt                                                               <  2:543978/150‑1 (MQ=255)
                                                                                        atatTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAAc                                                         >  2:187001/1‑150 (MQ=255)
                                                                                                ttCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGAAAGTGAAGGGGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCag                                                  <  1:7664/149‑1 (MQ=255)
                                                                                                      ataatGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGAt                                          >  1:412594/1‑151 (MQ=255)
                                                                                                       taatGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGAtt                                         >  1:839392/1‑151 (MQ=255)
                                                                                                       taagGTTTCATCCGTGAGCGAATCATCTGTCAACTAAATGACAATTGAAGGAGACATAGGTCATAAAAAGGGATATTACAGAAAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGAt                                          <  1:168546/150‑1 (MQ=255)
                                                                                                              tCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGtt                                  >  1:375621/1‑151 (MQ=255)
                                                                                                               cATCCGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTg                                 >  2:616575/1‑151 (MQ=255)
                                                                                                                  ccGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATGGGTAATACAAAGGGATTTTAAAGAAAAAAAACCCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGtt                                  <  1:241540/147‑1 (MQ=255)
                                                                                                                  ccGTGAGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTg                              >  1:435043/1‑151 (MQ=255)
                                                                                                                      gAGCGCATCATCTGTCAACTAAATGGAAAGTGAAGGGGGCATAGGTCATAAAAATGGATATTACAGAAAAAAAACCCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATac                          <  1:696161/151‑1 (MQ=255)
                                                                                                                      gAGCGAATCATCTGTAAACAAAATGGAAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATac                          <  1:286002/151‑1 (MQ=255)
                                                                                                                       aGCGCATCATCTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATacg                         >  2:564531/1‑151 (MQ=255)
                                                                                                                         cgcATCATCTGTCAACTAAATGGCAAGTGAGGGAGGCATAGGTCATAAAAATGTATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATacgac                       <  2:759375/151‑1 (MQ=255)
                                                                                                                          gcATAATCTGTCAACTAAATGGCAAGAGAAGGAGGCATAGGTCATACAAATGGATCTTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCCGAGATCGATTCTACGTTGCTGATacgcc                       >  1:811270/1‑148 (MQ=255)
                                                                                                                            atcatcTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATAcgacga                     >  2:326553/1‑150 (MQ=255)
                                                                                                                             tcatcTGTCAACAAAAGGGAAAGGGAAGGAGCCATAGGTCATACAAAGGGATATTACAGAAAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATacgacg                      <  1:30229/148‑1 (MQ=255)
                                                                                                                               atcTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCg                 >  2:436289/1‑151 (MQ=255)
                                                                                                                                tcTGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGc                >  1:389022/1‑151 (MQ=255)
                                                                                                                                  tGTCAACTAAATGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGAAAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGCt               <  2:230538/150‑1 (MQ=255)
                                                                                                                                      aaCAAAATGGCAATAGAAGGAGGCATAGGTAATAAAAATGGATATTACAGAAAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGCTTCgg           <  1:839610/150‑1 (MQ=255)
                                                                                                                                      aaCAAAATGGCAAGTGAAGGGGGCATAGGTCATAAAAATGAATATTACAGAAAAAAAACCCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGc                <  2:766125/145‑1 (MQ=255)
                                                                                                                                          aaaTGGCAGGGAAAGGAGGCATAGGTCAAACAAATGAATATTACAGACAAAAAACCCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGCTTCGGCCAGc      <  2:70777/151‑1 (MQ=255)
                                                                                                                                          aaaTGGCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGCTTCGGCCAGc      >  2:760031/1‑151 (MQ=255)
                                                                                                                                              ggCAAGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGCTTCGGCCAGCATAc  >  1:736386/1‑151 (MQ=255)
                                                                                                                                                  |                                                                                                                                                  
ATCAGGTCACGGGTAAACCGTGCGGCAGTATATTTTTCTTTCCAGCAAGCGTCGATCAGAGCGCGGAAAGGCATCACATGTGAGGAAAATATTTTGTTCACAATAATGTTTCATCCGTGAGCGCATCATCTGTCAACTAAATGGCAGGTGAAGGAGGCATAGGTCATACAAATGGATATTACAGACAAAAAAACCCGCCGCAGCGGGTCTTTGAGCCGGGTTCGATTAGTGTTCGAACATGGCAGAGATCGATTCTTCGTTGCTGATACGACGAATCGCTTCGGCCAGCATAC  >  NC_000913/1260703‑1260995

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A