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 1,568,594 A→C 26.7% T244T (ACT→ACG)  mntH ← manganese/divalent cation transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,568,5940AC26.7% 104.2 / 48.4 86T244T (ACT→ACG) mntHmanganese/divalent cation transporter
Reads supporting (aligned to +/- strand):  ref base A (30/33);  new base C (14/9);  total (44/42)
Fisher's exact test for biased strand distribution p-value = 3.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.47e-01

TGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTA  >  minE/1568529‑1568658
                                                                 |                                                                
tGACCGGAAAAGTGGAACGCCGCCTCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATATTc                                                               >  1:1918789/1‑69 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTGGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               >  1:1624205/1‑69 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               >  1:106767/1‑69 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               >  1:1082840/1‑69 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               <  1:637352/69‑1 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               <  1:3301356/69‑1 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               >  1:2570421/1‑69 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               <  1:1199127/69‑1 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               >  1:2562181/1‑69 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               <  1:2162344/69‑1 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               <  1:2085217/69‑1 (MQ=255)
tGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               >  1:196600/1‑69 (MQ=255)
 gACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               <  1:258586/68‑1 (MQ=255)
 gACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTc                                                               <  1:822646/68‑1 (MQ=255)
  aCCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTCAt                                                             >  1:717458/1‑69 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:2467142/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:3407799/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:514709/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:2747199/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:100905/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:1201065/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:763846/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:826579/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:2211607/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:863472/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:122337/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:2136709/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:2037509/1‑67 (MQ=255)
       aaaaGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGc                                                          >  1:956618/1‑67 (MQ=255)
                        gcAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:1259417/69‑1 (MQ=255)
                        gcAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:3418465/69‑1 (MQ=255)
                        gcAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:1151637/69‑1 (MQ=255)
                        gcAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:242075/69‑1 (MQ=255)
                        gcAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:1914699/69‑1 (MQ=255)
                        gcAGCTGTAGCCATCATCGCCAGATTGACAAAAACGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:1100645/69‑1 (MQ=255)
                         cAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:3064718/68‑1 (MQ=255)
                         cAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:678581/68‑1 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:1642593/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:1342809/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:3431178/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:2965104/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:1439098/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:2840292/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:627241/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:1450213/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:2752904/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:184922/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:68436/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:1711611/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:1738735/1‑68 (MQ=255)
                                 gCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGa                               >  1:2482578/1‑68 (MQ=255)
                                     tcatcGCCAGATTGACAAAACCGGCAATAGTCATGGc                                                          >  1:1085626/1‑37 (MQ=255)
                                     tcatcGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAAc                          >  1:16699/1‑69 (MQ=255)
                                     tcatcGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAAc                          >  1:1745787/1‑69 (MQ=255)
                                     tcatcGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAAc                          >  1:1382604/1‑69 (MQ=255)
                                     tcatcGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAAc                          >  1:955782/1‑69 (MQ=255)
                                     tcatcGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAAc                          >  1:829354/1‑69 (MQ=255)
                                         cGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACgtt                       <  1:284237/68‑1 (MQ=255)
                                          gCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACgttgt                     <  1:2682376/69‑1 (MQ=255)
                                          gCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACgttgt                     <  1:1744958/69‑1 (MQ=255)
                                          gCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACgttgt                     <  1:2911418/69‑1 (MQ=255)
                                          gCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACgttgt                     <  1:3296876/69‑1 (MQ=255)
                                          gCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACgttg                      >  1:2771702/1‑68 (MQ=255)
                                          gCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACgttg                      >  1:1165698/1‑68 (MQ=255)
                                             aGATTGACAAAACCGGCAATCGTCATGGCGATAGCCACATCCCATTtg                                       <  1:53476/48‑1 (MQ=255)
                                                       aaCCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGc        <  1:3363563/69‑1 (MQ=255)
                                                       aaCCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGc        <  1:2168795/69‑1 (MQ=255)
                                                       aaCCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGc        <  1:764515/69‑1 (MQ=255)
                                                       aaCCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGc        <  1:2826194/69‑1 (MQ=255)
                                                       aaCCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGc        <  1:254123/69‑1 (MQ=255)
                                                         ccGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGc        <  1:2449491/67‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:3307361/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:1927537/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:24205/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:2451411/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:2604778/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:2682725/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:674195/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:2699389/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:616842/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:544457/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:527661/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:2923455/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:486737/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:3059103/69‑1 (MQ=255)
                                                             cAATAGTCATGGCGATAGCCACATCCCATTTCGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTa  <  1:1585937/69‑1 (MQ=255)
                                                                 |                                                                
TGACCGGAAAAGTGGAACGCCGCCGCAGCTGTAGCCATCATCGCCAGATTGACAAAACCGGCAATAGTCATGGCGATAGCCACATCCCATTTGGTGGCGGAATAACGTTGTTGACGCGAACCGCCATGTA  >  minE/1568529‑1568658

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