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 920,281 C→T 47.8% L106L (TTG→TTA)  mpaA ← murein peptide amidase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE920,2810CT47.8% 10.4 / 100.7 115L106L (TTG→TTA) mpaAmurein peptide amidase A
Reads supporting (aligned to +/- strand):  ref base C (43/17);  new base T (39/16);  total (82/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.74e-01

Only 100 of 115 total aligned reads displayed.

CGCCGCCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTCAACG  >  minE/920227‑920345
                                                      |                                                                
cgccgtCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:2548796/1‑69 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGcc                                                       >  1:835796/1‑66 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:1001396/1‑69 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:447572/1‑69 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:1458261/1‑69 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:140752/1‑69 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:1284957/1‑69 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:3061524/1‑69 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:1389198/1‑69 (MQ=255)
cgccgcCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTc                                                    >  1:1407151/1‑69 (MQ=255)
   cgccgGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAgg                                                 >  1:706377/1‑69 (MQ=255)
                     tAAATCCACACCATTAGCATTGGCCCGTAACCCCa                                                                 <  1:1937557/35‑1 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACt                                                              >  1:2172568/1‑37 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcacgac                               >  1:1879180/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:2423527/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:2041567/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:2604057/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:2978455/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:3346252/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:1803257/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:1779856/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:2961808/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:1689565/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:1622595/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:1535285/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:3231881/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:3000457/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:723518/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:3073949/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:956640/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:1070934/1‑68 (MQ=255)
                      aaaTCCACACCATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGcaccac                               >  1:966622/1‑68 (MQ=255)
                          ccACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACatgat                          <  1:332037/69‑1 (MQ=255)
                          ccACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACatgat                          <  1:2112744/69‑1 (MQ=255)
                           cacaCCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGAt                                               >  1:2063132/1‑47 (MQ=255)
                           cacaCCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACatgatg                         >  1:2760135/1‑69 (MQ=255)
                           cacaCCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACatgatg                         >  1:2253595/1‑69 (MQ=255)
                           cacaCCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACatgatg                         >  1:33776/1‑69 (MQ=255)
                           cacaCCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACatgatg                         >  1:601132/1‑69 (MQ=255)
                           cacaCCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGAATCACACACAGCACCACatgatg                         >  1:2042268/1‑69 (MQ=255)
                               ccATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCgg                     <  1:2164305/69‑1 (MQ=255)
                               ccATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCgg                     <  1:2194438/69‑1 (MQ=255)
                               ccATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCgg                     <  1:476617/69‑1 (MQ=255)
                               ccATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCgg                     <  1:2782723/69‑1 (MQ=255)
                               ccATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCgg                     <  1:324947/69‑1 (MQ=255)
                                cATTAGCATTGGCCCGTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCgg                     <  1:3189570/68‑1 (MQ=255)
                                cATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCgg                     <  1:413081/68‑1 (MQ=255)
                                     gCATTGGCCCGTAAGCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACatgatgcgg                      <  1:1804706/62‑4 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            <  1:3108140/69‑1 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            >  1:1788082/1‑69 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            >  1:637091/1‑69 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            >  1:1340749/1‑69 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            >  1:3231695/1‑69 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            >  1:208983/1‑69 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            <  1:3395955/69‑1 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            <  1:189931/69‑1 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            <  1:2331819/69‑1 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            >  1:2326075/1‑69 (MQ=255)
                                        ttGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAaagaa            >  1:3403504/1‑69 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacacac                                       >  1:2610076/1‑40 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacacac                                       <  1:3255548/40‑1 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacacac                                       <  1:2876745/40‑1 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacacac                                       >  1:602294/1‑40 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacacac                                       >  1:299334/1‑40 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacacac                                       >  1:2021941/1‑40 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacacac                                       >  1:1326535/1‑40 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacacac                                       <  1:725694/40‑1 (MQ=255)
                                          ggCCCGTAACCCCAACTGGCAGCCGTCAGGATTcacaca                                        >  1:532566/1‑39 (MQ=255)
                                              cGTAACCCCAACTGTCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTc      >  1:559290/1‑69 (MQ=255)
                                              cGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTc      >  1:2676900/1‑69 (MQ=255)
                                              cGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTc      >  1:299942/1‑69 (MQ=255)
                                              cGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTc      >  1:1179222/1‑69 (MQ=255)
                                              cGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTc      >  1:2686259/1‑69 (MQ=255)
                                              cGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTc      >  1:1825369/1‑69 (MQ=255)
                                              cGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTc      >  1:1827228/1‑69 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTcacacac                                       >  1:830159/1‑35 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:1039746/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:1084515/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:941457/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:1131508/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:1463846/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:409116/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:2873168/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:2322887/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:2787902/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGgtgt       >  1:2726594/1‑67 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGGTGTCa     <  1:2311809/69‑1 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGGTGTCa     <  1:3247688/69‑1 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGGTGTCa     <  1:907838/69‑1 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGGTGTCa     <  1:1090285/69‑1 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGGTGTCa     <  1:2198039/69‑1 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGGCGGCGCAAAGACGGTGTCa     <  1:2223533/69‑1 (MQ=255)
                                               gTAACCCTAACTGGCAGCCGTCAGGATTCACACACAGCACCAAATGATGgcggcg                   >  1:377522/1‑55 (MQ=255)
                                                  aCCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACat                             <  1:125849/42‑1 (MQ=255)
                                                  aCCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACat                             <  1:2766038/42‑1 (MQ=255)
                                                  aCCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACat                             <  1:1609917/42‑1 (MQ=255)
                                                  aCCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACat                             <  1:1763115/42‑1 (MQ=255)
                                                  aCCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACat                             <  1:2828684/42‑1 (MQ=255)
                                                  aCCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTCAACg  >  1:66984/1‑69 (MQ=255)
                                                  aCCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTCAACg  >  1:3312060/1‑69 (MQ=255)
                                                      |                                                                
CGCCGCCGGAAAGTTTCTGTTTAAATCCACACCATTAGCATTGGCCCGTAACCCCAACTGGCAGCCGTCAGGATTCACACACAGCACCACATGATGACGGCGCAAAGAAGGTGTCAACG  >  minE/920227‑920345

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A