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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 936,797 G→A 22.1% S119S (TCG→TCA)  fdnI → formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE936,7970GA22.1% 245.4 / 52.7 171S119S (TCG→TCA) fdnIformate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible
Reads supporting (aligned to +/- strand):  ref base G (62/71);  new base A (26/12);  total (88/83)
Fisher's exact test for biased strand distribution p-value = 2.64e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

Only 100 of 172 total aligned reads displayed.

AGGCAATGAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAGTA  >  minE/936731‑936865
                                                                  |                                                                    
aGGCAATGAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGAt                                                                    <  1:2928120/69‑1 (MQ=255)
  gCAATGAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATc                                                                   >  1:2151249/1‑68 (MQ=255)
  gCAATGAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATc                                                                   >  1:436594/1‑68 (MQ=255)
  gCAATGAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATc                                                                   >  1:258695/1‑68 (MQ=255)
      tGAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAg                                                              <  1:2450887/69‑1 (MQ=255)
       gAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGc                                                             <  1:1960626/69‑1 (MQ=255)
       gAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGc                                                             <  1:2730579/69‑1 (MQ=255)
       gAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGc                                                             <  1:2855349/69‑1 (MQ=255)
        aGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGc                                                             >  1:1008900/1‑68 (MQ=255)
            tAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATc                                                                   >  1:2251479/1‑58 (MQ=255)
            tAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATc                                                                   >  1:2322044/1‑58 (MQ=255)
            tAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATc                                                                   >  1:2063400/1‑58 (MQ=255)
            tAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATc                                                                   >  1:200791/1‑58 (MQ=255)
            tAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATc                                                                   >  1:1704934/1‑58 (MQ=255)
             aaaGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAg                                                              <  1:2909739/62‑1 (MQ=255)
             aaaGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAg                                                              <  1:1698938/62‑1 (MQ=255)
              aaGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGAttt                                                      >  1:1063672/1‑69 (MQ=255)
              aaGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGAttt                                                      >  1:3423862/1‑69 (MQ=255)
              aaGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGAttt                                                      >  1:322777/1‑69 (MQ=255)
              aaGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGAtt                                                       >  1:1336245/1‑68 (MQ=255)
                     ggATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGtgct                                               <  1:2313087/69‑1 (MQ=255)
                     ggATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGtgct                                               <  1:2577381/69‑1 (MQ=255)
                     ggATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGtgct                                               <  1:2542588/69‑1 (MQ=255)
                     ggATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGttct                                               >  1:1582631/1‑69 (MQ=255)
                     ggATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGtgct                                               >  1:1425182/1‑69 (MQ=255)
                     ggATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGtgct                                               >  1:2798409/1‑69 (MQ=255)
                     ggATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGtgct                                               >  1:2110942/1‑69 (MQ=255)
                        tGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTgctgct                                            <  1:1837421/69‑1 (MQ=255)
                        tGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTgctgct                                            >  1:3372035/1‑69 (MQ=255)
                        tGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTgctgct                                            >  1:3157596/1‑69 (MQ=255)
                        tGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTgctgct                                            >  1:2702227/1‑69 (MQ=255)
                                  tACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:1439101/1‑69 (MQ=255)
                                  tACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:3035871/1‑69 (MQ=255)
                                  tACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:2457304/1‑69 (MQ=255)
                                  tACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:1752189/1‑69 (MQ=255)
                                   aCAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:2617401/1‑68 (MQ=255)
                                   aCAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:79657/1‑68 (MQ=255)
                                   aCAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:2661393/1‑68 (MQ=255)
                                   aCAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:2913962/1‑68 (MQ=255)
                                   aCAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:1036188/1‑68 (MQ=255)
                                   aCAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:2177211/1‑68 (MQ=255)
                                   aCAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCggg                                  >  1:2038690/1‑68 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATg                                                          <  1:757075/43‑1 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATg                                                          <  1:653844/43‑1 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATg                                                          <  1:691982/43‑1 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATg                                                          <  1:1068415/43‑1 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATg                                                          <  1:2033567/43‑1 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATg                                                          <  1:232506/43‑1 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATg                                                          <  1:2106053/43‑1 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGt                                >  1:2645247/1‑69 (MQ=255)
                                    cAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACAGGGGt                                >  1:176011/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:1369050/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:31871/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:2981727/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:1168608/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:1444764/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:3256345/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:3263424/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:1515590/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:1550136/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:171127/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:2630346/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:666398/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:243821/1‑69 (MQ=255)
                                       cGCCGGGCAAAAGATGATATTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGAt                             >  1:862254/1‑69 (MQ=255)
                                           gggCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGATTATc                         <  1:569020/69‑1 (MQ=255)
                                           gggCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGATTATc                         <  1:532838/69‑1 (MQ=255)
                                           gggCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGATTATc                         <  1:621179/69‑1 (MQ=255)
                                           gggCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGATTATc                         <  1:1206162/69‑1 (MQ=255)
                                           gggCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGATTATc                         <  1:3010799/69‑1 (MQ=255)
                                           gggCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGATTATc                         <  1:1666512/69‑1 (MQ=255)
                                           gggCAAAAGATGATGTTCTGGTCAATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGAGTGATTATc                         <  1:2972919/69‑1 (MQ=255)
                                             gCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTTCTGGTGACCGGGGTGATTATCTg                       <  1:1141148/69‑1 (MQ=255)
                                             gCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTg                       <  1:1455318/69‑1 (MQ=255)
                                             gCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTg                       <  1:604910/69‑1 (MQ=255)
                                             gCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTg                       <  1:2968661/69‑1 (MQ=255)
                                             gCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTg                       <  1:308241/69‑1 (MQ=255)
                                             gCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTg                       <  1:1236106/69‑1 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTgg                      >  1:773253/1‑69 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTgg                      >  1:2562800/1‑69 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTgg                      >  1:3316805/1‑69 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTgg                      >  1:1097634/1‑69 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTgg                      >  1:401671/1‑69 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTgg                      >  1:1713775/1‑69 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTg                       >  1:3126897/1‑68 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTg                       <  1:509704/68‑1 (MQ=255)
                                              cAAAAGATGATGTTCTGGTCGATCATGAGCATGATTATCGTGCTGCTGGTg                                        >  1:2742601/1‑51 (MQ=255)
                                                  aGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTc                  <  1:287819/69‑1 (MQ=255)
                                                    atgatgTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCg                <  1:4748/69‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTGGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:2750882/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:2788064/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:2281167/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:1081168/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:1873666/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:138261/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:3191152/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:1883471/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:829083/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:2408709/68‑1 (MQ=255)
                                                                 cGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAg    <  1:929835/68‑1 (MQ=255)
                                                                  |                                                                    
AGGCAATGAGCATAAAGTGGCGGATGTCGGTAAGTACAACGCCGGGCAAAAGATGATGTTCTGGTCGATCATGAGCATGATTTTCGTGCTGCTGGTGACCGGGGTGATTATCTGGCGTCCGTACTTTGCGCAGTA  >  minE/936731‑936865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A