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 2,720,333 C→T 31.8% V416V (GTG→GTA)  yhfK ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,720,3330CT31.8% 65.7 / 36.0 76V416V (GTG→GTA) yhfKconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (19/32);  new base T (14/10);  total (33/43)
Fisher's exact test for biased strand distribution p-value = 1.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGGGAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGT  >  minE/2720265‑2720400
                                                                    |                                                                   
tCGGGAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTc                                                                     <  1:1007342/69‑1 (MQ=255)
   ggAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTcac                                                                   <  1:152397/68‑1 (MQ=255)
   ggAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTcac                                                                   <  1:1938975/68‑1 (MQ=255)
   ggAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTcac                                                                   <  1:682640/68‑1 (MQ=255)
   ggAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTcac                                                                   <  1:579447/68‑1 (MQ=255)
   ggAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTcac                                                                   <  1:536093/68‑1 (MQ=255)
   ggAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTcac                                                                   <  1:532156/68‑1 (MQ=255)
   ggAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTcac                                                                   <  1:2934102/68‑1 (MQ=255)
   ggAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTcac                                                                   <  1:3066527/68‑1 (MQ=255)
    gAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACaa                                                                 <  1:2720621/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:298140/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:3040124/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:3053524/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:2187971/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:3147892/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:3197944/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:3353869/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:1331355/69‑1 (MQ=255)
       ttttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATcc                                                              <  1:751090/69‑1 (MQ=255)
        tttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCTCAATcc                                                              <  1:436153/68‑1 (MQ=255)
         ttAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATc                                                               >  1:445103/1‑66 (MQ=255)
               tGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACgg                                                      >  1:736617/1‑69 (MQ=255)
               tGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACgg                                                      >  1:1106028/1‑69 (MQ=255)
               tGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACg                                                       >  1:66427/1‑68 (MQ=255)
                 cAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGt                                                    >  1:1339566/1‑69 (MQ=255)
                 cAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGt                                                    >  1:2434551/1‑69 (MQ=255)
                 cAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGt                                                    >  1:927143/1‑69 (MQ=255)
                      ccACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTgcgc                                               <  1:138613/69‑1 (MQ=255)
                      ccACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTgcgc                                               <  1:624733/69‑1 (MQ=255)
                            ccGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGc                                         <  1:175096/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:341994/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:113358/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:2845538/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:2621841/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:1015983/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:3293421/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:146342/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:2170290/69‑1 (MQ=255)
                                  tGATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:1610897/69‑1 (MQ=255)
                                   gATTAACCCGACCACGGTTCCCACGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCAtttt                                   <  1:905708/68‑1 (MQ=255)
                                   gATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCAttttc                                  >  1:744218/1‑68 (MQ=255)
                                   gATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtg                                  >  1:2313264/1‑69 (MQ=255)
                                   gATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtg                                  >  1:1013968/1‑69 (MQ=255)
                                   gATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtg                                  >  1:3169996/1‑69 (MQ=255)
                                   gATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtg                                  >  1:2141938/1‑69 (MQ=255)
                                    aTTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtgt                                 >  1:3113722/1‑69 (MQ=255)
                                    aTTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtgt                                 >  1:1636799/1‑69 (MQ=255)
                                    aTTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtgt                                 >  1:305749/1‑69 (MQ=255)
                                    aTTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtgt                                 >  1:3026424/1‑69 (MQ=255)
                                    aTTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtgt                                 >  1:137918/1‑69 (MQ=255)
                                    aTTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtgt                                 >  1:1234464/1‑69 (MQ=255)
                                    aTTAACCCGACCACGGTTCCCACGGAGAGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTtgt                                 >  1:1773514/1‑69 (MQ=255)
                                             aCCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGc                        <  1:3146904/69‑1 (MQ=255)
                                             aCCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGc                        <  1:1755096/69‑1 (MQ=255)
                                             aCCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGc                        <  1:1284145/69‑1 (MQ=255)
                                                aCGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:2158577/69‑1 (MQ=255)
                                                 ctgTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:900728/66‑1 (MQ=255)
                                                      cccACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:700163/63‑1 (MQ=255)
                                                      cccACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:462586/63‑1 (MQ=255)
                                                      cccACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:3361961/63‑1 (MQ=255)
                                                      cccACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:1009251/63‑1 (MQ=255)
                                                      cccACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:1086815/63‑1 (MQ=255)
                                                      cccACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:1355953/63‑1 (MQ=255)
                                                      cccACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:226138/63‑1 (MQ=255)
                                                      accACGGAGCGATTAACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAAt                     <  1:3286251/62‑1 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGCCGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:106501/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTgcgt                               >  1:2437737/1‑49 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:2461711/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:1509006/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:1600094/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:1850022/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:2098735/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:598974/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:2562830/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:523006/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:2971193/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtcatc            >  1:297383/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGCGTCACCAGCAATACTGtaatc            >  1:886134/1‑68 (MQ=255)
                                                          cGGAGCGATTTACAATCCTCAGACGGGTTGCCCCATAGCCATTTTGCGTCAcc                           >  1:2774786/1‑53 (MQ=255)
                                                          cGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGc                                         <  1:982118/39‑1 (MQ=255)
                                                            gAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAgg         <  1:3316272/69‑1 (MQ=255)
                                                             aGCGATTCACACTCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGa        <  1:912907/69‑1 (MQ=255)
                                                             aGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGa        <  1:862371/69‑1 (MQ=255)
                                                             aGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGa        <  1:1371769/69‑1 (MQ=255)
                                                             aGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGa        <  1:2816951/69‑1 (MQ=255)
                                                                    cacaATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGt  >  1:2047236/1‑68 (MQ=255)
                                                                    cacaATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGt  >  1:3316049/1‑68 (MQ=255)
                                                                    |                                                                   
TCGGGAATTTTAAAGTGCAGCGCCACGCCCGCAATGATTAACCCGACCACGGTTCCCACGGAGCGATTCACAATCCTCAGACGGGTTGCGCCATAGCCATTTTGTGTCACCAGCAATACCGTCATCAGGATCCAGT  >  minE/2720265‑2720400

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