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 1,930,883 G→A 27.6% G93G (GGC→GGT)  kduI ← predicted 5‑keto 4‑deoxyuronate isomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,930,8830GA27.6% 143.8 / 50.2 126G93G (GGC→GGT) kduIpredicted 5‑keto 4‑deoxyuronate isomerase
Reads supporting (aligned to +/- strand):  ref base G (39/52);  new base A (14/21);  total (53/73)
Fisher's exact test for biased strand distribution p-value = 8.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 126 total aligned reads displayed.

GACAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTCGCGACGTTCAAGGA  >  minE/1930820‑1930947
                                                               |                                                                
gACAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGGCATc                                                             >  1:31956/1‑69 (MQ=255)
gACAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATc                                                             >  1:2012326/1‑69 (MQ=255)
gACAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATc                                                             >  1:2245510/1‑69 (MQ=255)
gACAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATc                                                             >  1:2533422/1‑69 (MQ=255)
gACAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATc                                                             >  1:2948643/1‑69 (MQ=255)
 aCAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCg                                                            <  1:3364575/69‑1 (MQ=255)
 aCAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCg                                                            <  1:1364088/69‑1 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAg                                                        >  1:637115/1‑68 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:3022536/1‑69 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:2131715/1‑69 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:31884/1‑69 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:1934253/1‑69 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:2667552/1‑69 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:1524845/1‑69 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:1837419/1‑69 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:2609724/1‑69 (MQ=255)
      ttcttTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGACCATCGACAGt                                                       >  1:1805717/1‑69 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  <  1:2829989/67‑1 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  <  1:1379570/67‑1 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  <  1:907227/67‑1 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  <  1:897997/67‑1 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  <  1:2956304/67‑1 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGt                                                 <  1:57249/68‑1 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGt                                                 <  1:180125/68‑1 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGt                                                 <  1:2629432/68‑1 (MQ=255)
             gCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGt                                                 <  1:2733577/68‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCAGCGCCaa                                   <  1:4575/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:2468699/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   >  1:2440956/1‑69 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:2659997/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:223053/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:460651/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:2067700/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:2036939/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   >  1:1082533/1‑69 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:1984418/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:1326633/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:1574260/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:835236/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:1697550/69‑1 (MQ=255)
                          cATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:1844523/69‑1 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCTACAGTAATCGTACCGGCACCGCCAata                                 >  1:822956/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTAcc                                              >  1:543128/1‑56 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCCCCGCCAat                                  >  1:3334789/1‑68 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   >  1:2981750/1‑67 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAata                                 >  1:618552/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAata                                 >  1:3034649/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAata                                 >  1:1836881/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAata                                 >  1:2241129/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAata                                 >  1:256483/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAata                                 >  1:747755/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAata                                 >  1:1351921/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAata                                 >  1:464255/1‑69 (MQ=255)
                            tACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAat                                  >  1:1198918/1‑68 (MQ=255)
                              cAGGGCGTCGCGGTGACCGATTTCATAGCATTGGcc                                                                >  1:2208692/1‑36 (MQ=255)
                              cAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  >  1:3032042/1‑50 (MQ=255)
                              cAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  >  1:384408/1‑50 (MQ=255)
                              cAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  >  1:663284/1‑50 (MQ=255)
                              cAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCg                                                  >  1:1926893/1‑50 (MQ=255)
                              cAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATAtt                               >  1:1504372/1‑69 (MQ=255)
                              cAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATAtt                               >  1:1185910/1‑69 (MQ=255)
                              cAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATAtt                               >  1:3001021/1‑69 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:2448933/69‑1 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:385885/69‑1 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            >  1:3235595/1‑69 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:3226750/69‑1 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:1197388/69‑1 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:1724968/69‑1 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:403721/69‑1 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:564159/69‑1 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:467097/69‑1 (MQ=255)
                                 ggCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            >  1:80365/1‑69 (MQ=255)
                                  gCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:2928745/61‑1 (MQ=255)
                                   cGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:1311145/60‑1 (MQ=255)
                                    gTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAac                         <  1:1491722/69‑1 (MQ=255)
                                    gTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAac                         <  1:1949316/69‑1 (MQ=255)
                                       gcgGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAacac                       >  1:3309293/1‑68 (MQ=255)
                                             aCCGATTTCATAGCATTGATCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:1206480/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:908039/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:2990177/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:1158430/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:1268032/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:1546990/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:2400020/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:2498875/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:252239/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:2590175/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:2665778/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:2837877/69‑1 (MQ=255)
                                             aCCGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:3410717/69‑1 (MQ=255)
                                              ccGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:2897383/68‑1 (MQ=255)
                                              ccGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:1162829/68‑1 (MQ=255)
                                              ccGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:1148508/68‑1 (MQ=255)
                                               cGATTTCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:1931408/67‑1 (MQ=255)
                                                gATTTCATAGCATTGACCATCGACAGTATTCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:1937/66‑1 (MQ=255)
                                                  tttCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGAt                            <  1:1990405/52‑1 (MQ=255)
                                                  tttCATAGCATTGACCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTc                <  1:550513/64‑1 (MQ=255)
                                                       tAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCaa                                   <  1:1411227/40‑1 (MQ=255)
                                                           aTTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTCGCGACGTTCAAGGa  <  1:2508637/69‑1 (MQ=255)
                                                           aTTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTCGCGACGTTCAAGGa  <  1:677199/69‑1 (MQ=255)
                                                               |                                                                
GACAACTTCTTTTGCACCTTTACCAACATACAGGGCGTCGCGGTGACCGATTTCATAGCATTGGCCATCGACAGTAATCGTACCGGCACCGCCAATATTGATAACACCTAACTCGCGACGTTCAAGGA  >  minE/1930820‑1930947

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

GATK/CNVnator alignment

N/A