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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,986,542 A→G 26.9% L19L (TTG→CTG)  arcA ← DNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,986,5420AG26.9% 153.8 / 68.4 93L19L (TTG→CTG) arcADNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA
Reads supporting (aligned to +/- strand):  ref base A (31/37);  new base G (23/2);  total (54/39)
Fisher's exact test for biased strand distribution p-value = 3.66e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.20e-01

ATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCT  >  minE/2986477‑2986607
                                                                 |                                                                 
aTGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCgtgt                                                              >  1:3349668/1‑71 (MQ=255)
aTGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACgt                                                                <  1:127093/69‑1 (MQ=255)
aTGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACgt                                                                <  1:2437159/69‑1 (MQ=255)
  gCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTg                                                            >  1:730495/1‑71 (MQ=255)
  gCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTg                                                            >  1:3133693/1‑71 (MQ=255)
  gCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTg                                                            >  1:1530949/1‑71 (MQ=255)
   cATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGc                                                           <  1:3864833/71‑1 (MQ=255)
   cATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGc                                                           <  1:3440147/71‑1 (MQ=255)
     tttCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgt                                                         <  1:748866/71‑1 (MQ=255)
     tttCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgt                                                         <  1:1915803/71‑1 (MQ=255)
     tttCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgt                                                         <  1:2086428/71‑1 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       >  1:2146222/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       >  1:3460198/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       >  1:4034063/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       >  1:2922255/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtg                                                        >  1:3328155/1‑70 (MQ=255)
            gcCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTAcc                                                   <  1:122861/70‑1 (MQ=255)
             ccATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCg                                                          <  1:480628/62‑1 (MQ=255)
             ccATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCg                                                          <  1:654377/62‑1 (MQ=255)
               aTCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTg                                                            <  1:288654/58‑1 (MQ=255)
               aTCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTg                                                            <  1:3238334/58‑1 (MQ=255)
               aTCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTg                                                            <  1:3000963/58‑1 (MQ=255)
               aTCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTg                                                            <  1:3650283/58‑1 (MQ=255)
               aTCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTg                                                            <  1:604737/58‑1 (MQ=255)
                tCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAAc                                                                  <  1:33637/51‑1 (MQ=255)
                tCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAAc                                                                  <  1:113461/51‑1 (MQ=255)
                tCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACgt                                                                <  1:591691/53‑1 (MQ=255)
                 cTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCg                                                          >  1:1435736/1‑58 (MQ=255)
                 cTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCg                                                          >  1:2960818/1‑58 (MQ=255)
                 cTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTT‑AACGTGTTGCg                                                          >  1:589909/1‑57 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGt                                            >  1:1619536/1‑71 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGt                                            >  1:2072116/1‑71 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGt                                            >  1:2906887/1‑71 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGt                                            >  1:2109062/1‑71 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGt                                            >  1:529350/1‑71 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGt                                            >  1:3270173/1‑71 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       >  1:1425516/1‑60 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGt                                            >  1:3901645/1‑71 (MQ=255)
                  tGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGt                                            >  1:1499442/1‑71 (MQ=255)
                        ttCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACgt                                                                <  1:3962713/45‑1 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACg                                                                 >  1:320246/1‑42 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAAc                                     >  1:2695856/1‑70 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAAc                                     >  1:2741717/1‑70 (MQ=255)
                           gAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAAc                                     <  1:33475/69‑1 (MQ=255)
                              aaCATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                  >  1:1422590/1‑69 (MQ=255)
                              aaCATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATaa                                <  1:373144/71‑1 (MQ=255)
                              aaCATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATaa                                <  1:2104695/71‑1 (MQ=255)
                               aCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAg                               <  1:3392294/71‑1 (MQ=255)
                               aCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAg                               <  1:597251/71‑1 (MQ=255)
                                catcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       <  1:2688503/46‑1 (MQ=255)
                                catcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       <  1:108758/46‑1 (MQ=255)
                                catcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       <  1:2683655/46‑1 (MQ=255)
                                catcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                       <  1:1400561/46‑1 (MQ=255)
                                 atcatAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGaa                             >  1:801585/1‑71 (MQ=255)
                                 atcatAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGaa                             >  1:929452/1‑71 (MQ=255)
                                  tcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAAc                                                <  1:2116392/51‑1 (MQ=255)
                                  tcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAAc                                                <  1:1467486/51‑1 (MQ=255)
                                  tcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAAc                                                <  1:3438864/51‑1 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                  >  1:1396040/1‑63 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                  >  1:3727011/1‑63 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                  >  1:4101962/1‑63 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                  >  1:2562240/1‑63 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                  >  1:1922181/1‑63 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                  >  1:238395/1‑63 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCaa                                                 >  1:3426422/1‑48 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTc                                              >  1:933471/1‑51 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTc                                              >  1:1689070/1‑51 (MQ=255)
                                           tCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                  <  1:561701/56‑1 (MQ=255)
                                               cTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCt                 >  1:2190445/1‑69 (MQ=255)
                                               cTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTg                >  1:146945/1‑70 (MQ=255)
                                                ttCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGATtgt                          <  1:3895908/59‑1 (MQ=255)
                                                ttCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtgt                          <  1:1660249/59‑1 (MQ=255)
                                                ttCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtgt                          <  1:4016047/59‑1 (MQ=255)
                                                ttCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtgt                          <  1:3458697/59‑1 (MQ=255)
                                                 tCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCAt             >  1:1566480/1‑71 (MQ=255)
                                                  cGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATg            >  1:1882984/1‑71 (MQ=255)
                                                   gAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGt           <  1:1574541/71‑1 (MQ=255)
                                                   gAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGt           <  1:1750901/71‑1 (MQ=255)
                                                    aaaaTACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGt           <  1:920523/70‑1 (MQ=255)
                                                      aaTACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGttt         >  1:3036402/1‑70 (MQ=255)
                                                      aaTACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGttt         >  1:3811780/1‑70 (MQ=255)
                                                      aaTACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTg        >  1:1776614/1‑71 (MQ=255)
                                                      aaTACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTg        >  1:1234199/1‑71 (MQ=255)
                                                      aaTACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTg        >  1:504077/1‑71 (MQ=255)
                                                      aaTACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTg        >  1:784277/1‑71 (MQ=255)
                                                      aaTACTGTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTg        >  1:7519/1‑71 (MQ=255)
                                                         aCTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTa     >  1:3934187/1‑71 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCa              >  1:3444732/1‑58 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCa              >  1:764521/1‑58 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCt  >  1:1390384/1‑70 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCt  >  1:1385249/1‑70 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCt  >  1:3790528/1‑70 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGCGTCTGCa              >  1:3435459/1‑58 (MQ=255)
                                                                aaCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAg                               <  1:3577145/38‑1 (MQ=255)
                                                                 |                                                                 
ATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCT  >  minE/2986477‑2986607

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