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 1,590,206 C→T 31.8% V30V (GTG→GTA)  pdxK ← pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,590,2060CT31.8% 84.7 / 45.6 94V30V (GTG→GTA) pdxKpyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase
Reads supporting (aligned to +/- strand):  ref base C (28/36);  new base T (16/14);  total (44/50)
Fisher's exact test for biased strand distribution p-value = 5.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.17e-01

CCGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCTACTCTTATC  >  minE/1590142‑1590271
                                                                |                                                                 
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCAcac                                                               >  1:2386681/1‑67 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:505056/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:2450316/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:1233435/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:2442263/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:1278425/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:3371305/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:2279637/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:654906/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:1939344/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGc                                                               >  1:754515/1‑69 (MQ=255)
ccGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGAACGGCAATGCTGTTGCCCACGc                                                               >  1:664869/1‑69 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:3144646/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:3247908/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:3217622/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:3201491/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:3163290/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:1014918/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:3097843/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:3097264/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:2310296/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:3012700/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:1694564/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:931595/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:1300687/69‑1 (MQ=255)
     ggcacggcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCg                                                          <  1:1700223/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:3061734/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:2668825/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:265972/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:1033097/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:963677/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    >  1:2409253/1‑69 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:1241112/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:2369322/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:2325027/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    >  1:963185/1‑69 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:1320757/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:1986121/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:1508296/69‑1 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    >  1:721114/1‑69 (MQ=255)
           gcaAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAacc                                                    <  1:3296714/69‑1 (MQ=255)
                 aCATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAACCACCTGc                                              <  1:1346068/69‑1 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:952475/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:699167/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:673169/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:966011/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:2937041/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:2792020/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:348807/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:1021496/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:1782557/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:190322/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:1776221/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:2157055/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:1719880/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:2565071/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:1280841/1‑68 (MQ=255)
                           cGTTCTGTTTGATAGCAGGCACCGCAATGCTGTTGCCTACGCTGCCGTACACTACCTGCGACTGCACg                                     >  1:2642903/1‑68 (MQ=255)
                               cTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGt                                                         >  1:3033449/1‑44 (MQ=255)
                               cTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTa                                                        >  1:2989432/1‑45 (MQ=255)
                               cTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTa                                                        >  1:2801947/1‑45 (MQ=255)
                                    tGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGatat                           <  1:590927/69‑1 (MQ=255)
                                            ggCACGGCAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGc                   <  1:2043364/69‑1 (MQ=255)
                                             gCACGGCAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGc                   <  1:8485/68‑1 (MQ=255)
                                                   cAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGccc            <  1:1597921/69‑1 (MQ=255)
                                                   cAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGccc            <  1:877964/69‑1 (MQ=255)
                                                   cAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGccc            <  1:342629/69‑1 (MQ=255)
                                                   cAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGccc            <  1:3311843/69‑1 (MQ=255)
                                                   cAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGccc            <  1:1891308/69‑1 (MQ=255)
                                                   cAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGccc            <  1:2599912/69‑1 (MQ=255)
                                                   cAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGccc            <  1:2197535/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCTGCCTGCAGTGCCCt           <  1:2123042/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGGCCt           <  1:1648615/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:3285747/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:2754899/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:282304/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:146644/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:890682/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:2895360/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:532236/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:3393740/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:2705821/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCt           <  1:1879809/69‑1 (MQ=255)
                                                    aaTGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCACTGCCCt           <  1:3076925/69‑1 (MQ=255)
                                                        cTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTg               >  1:1669293/1‑61 (MQ=255)
                                                        cTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTg               >  1:1657116/1‑61 (MQ=255)
                                                        cTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTg               >  1:1522321/1‑61 (MQ=255)
                                                        cTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTg               >  1:182473/1‑61 (MQ=255)
                                                             gCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGatat                           >  1:1325834/1‑44 (MQ=255)
                                                             gCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCTACTCTTATc  >  1:3042206/1‑69 (MQ=255)
                                                             gCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCTACTCTTATc  >  1:1578103/1‑69 (MQ=255)
                                                             gCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCTACTCTTATc  >  1:411652/1‑69 (MQ=255)
                                                             gCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCTACTCTTATc  >  1:2015601/1‑69 (MQ=255)
                                                             gCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCTACTCTTATc  >  1:123720/1‑69 (MQ=255)
                                                                |                                                                 
CCGTCGGCACGGCAAAGACATTCAGGCCGTTCTGTTTGATAGCAGGCACGGCAATGCTGTTGCCCACGCTGCCGTAAACCACCTGCGACTGCACGGCGACGATATCCGCCTGCAGTGCCCTACTCTTATC  >  minE/1590142‑1590271

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