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 515,011 T→C 46.5% I234M (ATA→ATG)  bioA ← 7,8‑diaminopelargonic acid synthase, PLP‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE515,0110TC46.5% 8.0 / 87.9 101I234M (ATA→ATG) bioA7,8‑diaminopelargonic acid synthase, PLP‑dependent
Reads supporting (aligned to +/- strand):  ref base T (37/17);  new base C (23/24);  total (60/41)
Fisher's exact test for biased strand distribution p-value = 6.71e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 101 total aligned reads displayed.

TACGACCAAATCCAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTGCGCCCTGGACA  >  minE/514953‑515074
                                                          |                                                               
tACGACCAAATCCAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCgg                                                        >  1:759248/1‑68 (MQ=255)
tACGACCAAATCCAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGa                                                       >  1:1398114/1‑69 (MQ=255)
tACGACCAAATCCAGTCGCGATCTCCTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGa                                                       >  1:1351579/1‑69 (MQ=255)
    aCCAAATCCAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCg                                                   <  1:2110181/69‑1 (MQ=255)
           ccAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            <  1:1841002/69‑1 (MQ=255)
           ccAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            <  1:246625/69‑1 (MQ=255)
           ccAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            <  1:1528540/69‑1 (MQ=255)
           ccAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            <  1:223466/69‑1 (MQ=255)
           ccAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            <  1:2270392/69‑1 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:340960/1‑68 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:321099/1‑68 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:464019/1‑68 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:3109002/1‑68 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:2151541/1‑68 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:1503026/1‑68 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:238303/1‑68 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:1284253/1‑68 (MQ=255)
                 gCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTc                                       >  1:1240026/1‑68 (MQ=255)
                      ctcGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGAt                                  >  1:3073157/1‑68 (MQ=255)
                      ctcGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGAt                                  >  1:1492595/1‑68 (MQ=255)
                              cAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:2990711/68‑1 (MQ=255)
                              cAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:532579/68‑1 (MQ=255)
                              cAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:3373232/68‑1 (MQ=255)
                              cAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          >  1:2746340/1‑68 (MQ=255)
                               aaTCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATgcg                        <  1:3066735/69‑1 (MQ=255)
                               aaTCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATgcg                        <  1:73249/69‑1 (MQ=255)
                               aaTCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATgcg                        <  1:2271072/69‑1 (MQ=255)
                               aaTCAGCAAGATACCTTCCCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATgcg                        <  1:1693425/69‑1 (MQ=255)
                                 tCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCa                      <  1:540507/69‑1 (MQ=255)
                                 tCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCa                      <  1:1265642/69‑1 (MQ=255)
                                   aGCAAGATACCTTCTCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:2568512/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCTCATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:423867/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGAt                                                      >  1:1988750/1‑35 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:1816763/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:275438/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:2538435/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:2869675/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:662019/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:655950/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:1453523/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:444350/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:1716300/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAAc                                            >  1:3405948/1‑45 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTa                              >  1:1572266/1‑59 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATc                    >  1:1411715/1‑69 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATc                    >  1:1752439/1‑69 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATc                    >  1:1112339/1‑69 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATc                    >  1:2427824/1‑69 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTGCATg                          <  1:2850598/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:2972391/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:951662/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:835640/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:358144/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:690299/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:669192/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:1073349/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:6232/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:3106753/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:574360/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:1049269/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:2560097/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:2544669/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:1304235/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:1532312/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:2329234/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:1602726/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:1642280/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:1675135/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:2215070/63‑1 (MQ=255)
                                   aGCAAGATACCTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATg                          <  1:1940161/63‑1 (MQ=255)
                                            ccTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcg           >  1:1809765/1‑69 (MQ=255)
                                            ccTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcg           >  1:1302068/1‑69 (MQ=255)
                                            ccTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcg           >  1:1848298/1‑69 (MQ=255)
                                            ccTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcg           >  1:263116/1‑69 (MQ=255)
                                            ccTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcg           >  1:2934358/1‑69 (MQ=255)
                                            ccTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgc            >  1:337761/1‑68 (MQ=255)
                                             cTTCGCGATTGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:2565288/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCa                                          >  1:1574731/1‑37 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACAt                           >  1:3103615/1‑52 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:519712/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:1175884/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:2553433/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:2370950/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:1308995/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:662234/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:1431333/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:1480000/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:2325486/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:3138354/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:2274305/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:2233101/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:1724429/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:37079/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:1793901/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:2144504/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcgc          >  1:3170642/1‑69 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcg           >  1:1423669/1‑68 (MQ=255)
                                             cTTCGCGATCGCACATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTgcg           >  1:397877/1‑68 (MQ=255)
                                                     tCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTGCGCCCTGGACa  <  1:2141995/69‑1 (MQ=255)
                                                     tCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTGCGCCCTGGACa  <  1:1077970/69‑1 (MQ=255)
                                                          |                                                               
TACGACCAAATCCAGTGGCGATCTCGTCGGCAATCAGCAAGATACCTTCGCGATCGCATATTTTGCGGATTCGTTTTAACCATTCCGGATGGTACATGCGCATCCCGCCTGCGCCCTGGACA  >  minE/514953‑515074

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