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 1,977,655 C→T 41.9% N105N (AAC→AAT)  endA → DNA‑specific endonuclease I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,977,6550CT41.9% 63.4 / 114.2 155N105N (AAC→AAT) endADNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base C (39/51);  new base T (12/53);  total (51/104)
Fisher's exact test for biased strand distribution p-value = 1.67e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

Only 100 of 170 total aligned reads displayed.

TCGTTCCCGCCTGGCAGTTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCGGTGA  >  minE/1977594‑1977723
                                                             |                                                                    
tCGTTCCCGCCTGGCAGTTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTgcgc                                                                 >  1:798324/1‑67 (MQ=255)
    tCCTGCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAg                                                            <  1:2190982/68‑1 (MQ=255)
    tCCTGCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAg                                                            <  1:336609/68‑1 (MQ=255)
    tCCTGCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAg                                                            <  1:2253654/68‑1 (MQ=255)
    tCCTGCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAg                                                            <  1:3052540/68‑1 (MQ=255)
    tCCTGCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAg                                                            <  1:2981921/68‑1 (MQ=255)
    tCCTGCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAg                                                            <  1:1299929/68‑1 (MQ=255)
    tCCTGCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAg                                                            <  1:1016460/68‑1 (MQ=255)
    tCCCGCCTGGCAGTTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAg                                                            <  1:2478304/68‑1 (MQ=255)
     cctgCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGa                                                           >  1:2815313/4‑68 (MQ=255)
     cctgCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGAt                                                          >  1:345329/4‑69 (MQ=255)
     cctgCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGAt                                                          >  1:2275601/4‑69 (MQ=255)
     cctgCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGAt                                                          >  1:234160/4‑69 (MQ=255)
     cctgCCTGGCAATTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGAt                                                          >  1:393844/4‑69 (MQ=255)
     cccGCCTTGCAGTTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGAt                                                          >  1:559369/1‑69 (MQ=255)
     cccGCCTGGCAGTTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGAt                                                          >  1:2562089/1‑69 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:2502014/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:2621409/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:2752223/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:2283613/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:369139/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:3110976/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:3272718/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:2243254/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:170920/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:1439640/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:1393544/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:1385774/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:734577/57‑1 (MQ=255)
                  tCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:777226/57‑1 (MQ=255)
                   cGGTCACCAGCGCGAGTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:1494632/56‑1 (MQ=255)
                   cGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATc                                                >  1:2641147/1‑65 (MQ=255)
                   cGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATc                                                >  1:1845442/1‑65 (MQ=255)
                   cGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATc                                                >  1:318630/1‑65 (MQ=255)
                   cGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATc                                                >  1:1948746/1‑65 (MQ=255)
                   cGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATc                                                >  1:2148174/1‑65 (MQ=255)
                   cGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCAATc                                                >  1:2799235/1‑65 (MQ=255)
                          cAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGaa                                     >  1:2894710/1‑69 (MQ=255)
                          cAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGaa                                     >  1:833108/1‑69 (MQ=255)
                          cAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGaa                                     >  1:3382487/1‑69 (MQ=255)
                          cAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGaa                                     >  1:576707/1‑69 (MQ=255)
                          cAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGa                                      <  1:1767217/68‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:3414062/69‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:1341472/69‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:966673/69‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:925781/69‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:543303/69‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:2504773/69‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:478079/69‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:1612419/69‑1 (MQ=255)
                               ccAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:1649485/69‑1 (MQ=255)
                                cAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGat                               <  1:2318534/69‑1 (MQ=255)
                                cAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGATAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:2995638/68‑1 (MQ=255)
                                  gTGCTGGCAGGACGGTGGACGTAAAAATTGCGCCAAAGATc                                                         <  1:2943430/41‑1 (MQ=38)
                                    gCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAg                                                            >  1:1726278/1‑36 (MQ=255)
                                     cTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCt                                                   >  1:1485080/1‑44 (MQ=255)
                                     cTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGc                           >  1:2955833/1‑68 (MQ=255)
                                     cTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGc                           >  1:64577/1‑68 (MQ=255)
                                       ggCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:2212383/69‑1 (MQ=255)
                                       ggCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:151785/69‑1 (MQ=255)
                                       ggCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:3363280/69‑1 (MQ=255)
                                       ggCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:431469/69‑1 (MQ=255)
                                        gCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:2856732/68‑1 (MQ=255)
                                              gggtggtCGTAAAATCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCgt                                <  1:710054/53‑2 (MQ=255)
                                               ggTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAATCGa                                >  1:1451849/1‑53 (MQ=255)
                                               ggTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:690662/53‑1 (MQ=255)
                                               ggTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:54876/53‑1 (MQ=255)
                                               ggTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGa                                <  1:3337365/53‑1 (MQ=255)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:2669695/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:797179/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:943526/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:577468/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:1349896/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:1366765/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:1677092/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:1889839/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:2003168/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:2013868/50‑1 (MQ=38)
                                                     cGTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:2062728/50‑1 (MQ=38)
                                                      gTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:3160122/49‑1 (MQ=38)
                                                      gTAAAAATTGCGCCAAAGATCCGGTCTATCGCAAGATGGAAAGCGatat                             <  1:2775780/49‑1 (MQ=38)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:324234/51‑1 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:1056137/51‑1 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:3252523/51‑1 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:2761177/51‑1 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:2773752/51‑1 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATa                        <  1:3157555/51‑1 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCg      >  1:1027730/1‑69 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCg      >  1:2008063/1‑69 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCg      >  1:1188707/1‑69 (MQ=255)
                                                         aaaaCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCg      >  1:128868/1‑69 (MQ=255)
                                                            aCTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAAcc                     >  1:2557516/1‑51 (MQ=255)
                                                             cTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCggtga  <  1:3405892/69‑1 (MQ=255)
                                                             cTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCggtga  >  1:1506857/1‑69 (MQ=255)
                                                             cTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCggtga  <  1:1625294/69‑1 (MQ=255)
                                                             cTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCggtga  <  1:1084660/69‑1 (MQ=255)
                                                             cTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCggtga  <  1:873439/69‑1 (MQ=255)
                                                             cTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCggtga  >  1:1082361/1‑69 (MQ=255)
                                                             cTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCggtga  <  1:2685442/69‑1 (MQ=255)
                                                             cTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCggtga  <  1:2446091/69‑1 (MQ=255)
                                                             |                                                                    
TCGTTCCCGCCTGGCAGTTCGGTCACCAGCGCCAGTGCTGGCAGGACGGTGGACGTAAAAACTGCGCTAAAGATCCGGTCTATCGCAAGATGGAAAGCGATATGCATAACCTGCAGCCGTCAGTCGGTGA  >  minE/1977594‑1977723

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