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 1,966,812 A→G 38.4% T606T (ACT→ACC)  tktA ← transketolase 1, thiamin‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,966,8120AG38.4% 58.8 / 79.5 117T606T (ACT→ACC) tktAtransketolase 1, thiamin‑binding
Reads supporting (aligned to +/- strand):  ref base A (46/26);  new base G (22/23);  total (68/49)
Fisher's exact test for biased strand distribution p-value = 1.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 117 total aligned reads displayed.

TTCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTA  >  minE/1966753‑1966875
                                                           |                                                               
ttCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCt                                                        <  1:3360125/69‑1 (MQ=255)
             aCTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACgg                                           <  1:2683651/69‑1 (MQ=255)
              cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACgg                                           >  1:377830/1‑68 (MQ=255)
              cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                                          >  1:537404/1‑69 (MQ=255)
              cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                                          >  1:801063/1‑69 (MQ=255)
              cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                                          >  1:2338927/1‑69 (MQ=255)
              cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                                          >  1:1508768/1‑69 (MQ=255)
              cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                                          >  1:2753760/1‑69 (MQ=255)
              cTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGa                                          >  1:2969400/1‑69 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                            >  1:277648/1‑55 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                            >  1:273258/1‑55 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                            >  1:931623/1‑55 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                            >  1:616966/1‑55 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                            >  1:1885040/1‑55 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACg                                            >  1:3358979/1‑55 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCTCGGTAagc                              >  1:2917857/1‑69 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              <  1:355885/69‑1 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              <  1:1116979/69‑1 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              >  1:2881214/1‑69 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              <  1:2614879/69‑1 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              <  1:2414322/69‑1 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              <  1:2260922/69‑1 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              <  1:141516/69‑1 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              >  1:1550914/1‑69 (MQ=255)
                          gtCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAagc                              <  1:1695065/69‑1 (MQ=255)
                               cAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAgcagca                          <  1:548111/68‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:3324875/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:1290308/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:1372726/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:1101994/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:2825118/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:126422/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:557757/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:912374/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:2399533/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:3038477/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:2175773/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:3182777/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:1855013/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:1135545/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:344441/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:200444/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:3060681/58‑1 (MQ=255)
                                aaTGCCAGCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:2194653/58‑1 (MQ=255)
                                 aTACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATcc                       >  1:2072594/1‑69 (MQ=255)
                                 aTACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATcc                       >  1:2490924/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTg                     >  1:2080867/1‑68 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTg                     >  1:1454706/1‑68 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:2916187/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:1188079/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:1192939/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:350275/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:3107019/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:3333983/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:1271673/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:1815986/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:2273467/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:1732384/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:845724/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:714199/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:145970/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:888251/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:2356833/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:2561034/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:2590009/1‑69 (MQ=255)
                                    cccGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGc                    >  1:2642203/1‑69 (MQ=255)
                                    cccGCTTCTACAACAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAACATCCTGc                    >  1:1476233/1‑69 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:94475/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:68858/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:726337/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:2671674/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:361510/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:769279/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:77829/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:1477895/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:3065635/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:2965961/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:2863331/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:1807444/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:1854725/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:2565933/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagccgcg                          >  1:1980205/1‑59 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACGGTAagcc                             >  1:97092/1‑56 (MQ=255)
                                       gCTTCCACCGCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACAGTAagccgcg                          >  1:1516350/1‑59 (MQ=255)
                                          tCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCa              <  1:2871655/69‑1 (MQ=255)
                                          tCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCa              <  1:195973/69‑1 (MQ=255)
                                                gCAACACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:152796/42‑1 (MQ=37)
                                                  aaCACGAGCGGTAACCGCTTTCGGCAGTACGGATTCACgg                                   <  1:2272232/40‑1 (MQ=37)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCTTCGGTa  <  1:1872860/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:2147776/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:3125280/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:2560936/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:2696504/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:429323/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:1731270/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:2776047/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:369407/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:3088879/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:1154750/69‑1 (MQ=255)
                                                      cgTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTa  <  1:3097430/69‑1 (MQ=255)
                                                           |                                                               
TTCAGGCCAACATACTTGTACCAGTAGTCAGCAATACCCGCTTCTACAGCAACGCGTGCAGTAACCGCTTTCGGCAGTACGGATTCACGGTAAGCAGCATCCTGCTTGTCAAATGCGTCGGTA  >  minE/1966753‑1966875

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A