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
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,432,273 G→A A1075A (GCG→GCA)  stfR → Rac prophage, putative tail fiber protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,432,2730GA98.5% 200.0 / ‑5.4 65A1075A (GCG→GCA) stfRRac prophage, putative tail fiber protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (31/33);  minor base T (0/1);  total (31/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CTAGTGCTAACTCCGGTGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGT  >  NC_000913/1432140‑1432398
                                                                                                                                     |                                                                                                                             
cTAGTGCTAACTCCGGTGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATAc                                                                                                                          >  2:1233141/1‑139 (MQ=255)
    tGCTAACTCCGGTGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTc                                                                                                                      >  2:1337837/1‑139 (MQ=255)
         aCTCCGGTGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATGCTGTCGGTAt                                                                                                                 <  2:807485/139‑1 (MQ=255)
            ccGGTGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTgg                                                                                                              <  1:258235/139‑1 (MQ=255)
              ggTGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCTCATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTg                                                                                                            >  2:1145639/1‑139 (MQ=255)
              ggTGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTg                                                                                                            >  1:1362581/1‑139 (MQ=255)
                tGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCt                                                                                                          >  1:244675/1‑139 (MQ=255)
                               aacaaGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACt                                                                                                                         <  2:320700/109‑1 (MQ=255)
                               aacaaGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACt                                                                                                                         >  1:320700/1‑109 (MQ=255)
                                acaaGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTg                                                                                          >  1:668432/1‑139 (MQ=255)
                                      ttGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACt                                                                                                                         >  1:290206/1‑102 (MQ=255)
                                      ttGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACt                                                                                                                         <  2:290206/102‑1 (MQ=255)
                                         tCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATAc                                                                                                                          >  1:1295333/1‑98 (MQ=255)
                                         tCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATAc                                                                                                                          <  2:1295333/98‑1 (MQ=255)
                                         tCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGAt                                                                                      <  2:959041/134‑1 (MQ=255)
                                         tCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGAt                                                                                      >  1:959041/1‑134 (MQ=255)
                                         tCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGtt                                                                                 >  2:945191/1‑139 (MQ=255)
                                            gttgtGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTcac                                                                              <  2:668432/139‑1 (MQ=255)
                                             ttgtGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTcaca                                                                             <  2:244675/139‑1 (MQ=255)
                                                tgCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTCCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGAt                                                                                      >  2:844088/1‑127 (MQ=255)
                                                tgCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGATGCACACGCTCATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGAt                                                                                      <  1:844088/127‑1 (MQ=255)
                                                 gCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGa                                                                         <  1:508873/139‑1 (MQ=255)
                                                 gCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGa                                                                         <  1:291226/139‑1 (MQ=255)
                                                 gCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGa                                                                         <  1:1233141/139‑1 (MQ=255)
                                                  cATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGac                                                                        <  1:945191/139‑1 (MQ=255)
                                                       tCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACAcc                                                                   >  1:30999/1‑139 (MQ=255)
                                                                tGCAACATCATCTGCTGGCACACATACCCACTCACTGTCCTGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGa                                                                         >  2:833783/1‑124 (MQ=255)
                                                                tGCAACATCATCTGCTGGCACACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGa                                                                         <  1:833783/124‑1 (MQ=255)
                                                                 gCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTa                                                         >  2:559322/1‑139 (MQ=255)
                                                                  cAACATCATCTGCTGGCGCTCATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTaa                                                        <  1:1145639/139‑1 (MQ=255)
                                                                   aaCATCATCTGCTGGCGCATATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAAc                                                       <  1:400060/139‑1 (MQ=255)
                                                                               tgGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACTATc                                                                >  2:761819/1‑118 (MQ=255)
                                                                               tgGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATc                                                                <  1:761819/118‑1 (MQ=255)
                                                                               tgGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAAc                                           >  2:331269/1‑139 (MQ=255)
                                                                                  cgcACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACg                                                                                                    >  1:360747/1‑79 (MQ=255)
                                                                                  cgcACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACg                                                                                                    <  2:360747/79‑1 (MQ=255)
                                                                                    cacacaCCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGa                                      >  2:343075/1‑139 (MQ=255)
                                                                                    cacaTACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGa                                      >  1:846606/1‑139 (MQ=255)
                                                                                               tcactGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTg                                                                                                            >  1:635334/1‑58 (MQ=255)
                                                                                               tcactGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTg                                                                                                            <  2:635334/58‑1 (MQ=255)
                                                                                                 actGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTCCGATTGGTTCACATGGACACACCATCACCGTTAATGCTGCTGGTAACGCGGAAAACACCGACaaa                         >  1:422271/1‑139 (MQ=255)
                                                                                                   tGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCaaaaa                       >  1:889333/1‑139 (MQ=25)
                                                                                                   tGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCaaaaa                       >  2:298266/1‑139 (MQ=21)
                                                                                                   tGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCaaaaa                       >  2:203044/1‑139 (MQ=25)
                                                                                                     tCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGac                                                                        <  1:311369/88‑1 (MQ=255)
                                                                                                     tCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGac                                                                        >  2:311369/1‑88 (MQ=255)
                                                                                                     tCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTGAcg                                          >  2:765076/1‑118 (MQ=255)
                                                                                                     tCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAAcg                                          <  1:765076/118‑1 (MQ=21)
                                                                                                     tCCGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACa                     <  1:203044/139‑1 (MQ=37)
                                                                                                      ccGGCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTTAAAAACAt                    <  2:889333/139‑1 (MQ=19)
                                                                                                        ggCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACg                                                                                                    >  2:297412/1‑57 (MQ=255)
                                                                                                        ggCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACg                                                                                                    <  1:297412/57‑1 (MQ=255)
                                                                                                        ggCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACg                                                                                                    >  2:589428/1‑57 (MQ=255)
                                                                                                        ggCACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCg                  <  2:30999/139‑1 (MQ=25)
                                                                                                        ggCAATGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACg                                                                                                    <  1:589428/57‑1 (MQ=14)
                                                                                                          cACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCa                <  1:1180599/139‑1 (MQ=25)
                                                                                                          cACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCa                <  2:1362581/139‑1 (MQ=37)
                                                                                                          cACTGCTGCAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCa                <  1:1337837/139‑1 (MQ=21)
                                                                                                               ctgcAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCa                                                                                                  <  1:906230/52‑1 (MQ=255)
                                                                                                               ctgcAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCa                                                                                                  >  2:906230/1‑52 (MQ=255)
                                                                                                               ctgcAAGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTaa           <  1:331269/139‑1 (MQ=25)
                                                                                                                    aGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCaa                          <  2:67440/119‑1 (MQ=255)
                                                                                                                    aGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCaa                          >  1:67440/1‑119 (MQ=37)
                                                                                                                    aGCGCAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACtata      <  1:559322/139‑1 (MQ=25)
                                                                                                                        cAGGTGCACACGCACATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATtgt  <  1:298266/139‑1 (MQ=25)
                                                                                                                                     |                                                                                                                             
CTAGTGCTAACTCCGGTGCTGGTAGTGCATCAACAAGATTGTCTGTTGTGCATAATCAAAACTATGCAACATCATCTGCTGGCGCACATACCCACTCACTGTCCGGCACTGCTGCAAGCGCAGGTGCACACGCGCATACTGTCGGTATTGGTGCTCATACGCACTCCGTTGCGATTGGTTCACATGGACACACCATCACCGTTAACGCTGCTGGTAACGCGGAAAACACCGTCAAAAACATCGCATTTAACTATATTGT  >  NC_000913/1432140‑1432398

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A