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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,340,287 G→A L79F (CTT→TTT)  adiA ← arginine decarboxylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,340,2870GA98.4% 207.0 / ‑4.1 63L79F (CTT→TTT) adiAarginine decarboxylase
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (23/39);  total (23/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01

TCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAAGAGAG  >  NC_000913/4340193‑4340380
                                                                                              |                                                                                             
tCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTAc                                                                                          <  1:819907/100‑1 (MQ=255)
 cGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTAcc                                                                                         <  2:747054/100‑1 (MQ=255)
 cGAAAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTAcc                                                                                         <  2:437953/100‑1 (MQ=255)
  gACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCg                                                                                        <  2:1524683/100‑1 (MQ=255)
  gACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCg                                                                                        >  1:495995/1‑100 (MQ=255)
     aaGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATc                                                                                     <  1:489672/100‑1 (MQ=255)
      aGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCa                                                                                    <  2:289869/100‑1 (MQ=255)
       gCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCaa                                                                                   >  2:557421/1‑100 (MQ=255)
         tCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAAtt                                                                                 >  1:950288/1‑100 (MQ=255)
            agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                              <  2:399612/100‑1 (MQ=255)
            agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                              >  1:748884/1‑100 (MQ=255)
            agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                              <  1:716666/100‑1 (MQ=255)
            agcagGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTc                                                                              >  1:1269949/1‑100 (MQ=255)
                ggTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGAc                                                                          <  1:158969/100‑1 (MQ=255)
                ggTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGAc                                                                          <  1:1080773/100‑1 (MQ=255)
                ggTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGAc                                                                          >  2:544871/1‑100 (MQ=255)
                    gcgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGttt                                                                      <  2:274236/100‑1 (MQ=255)
                     cgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTGCCGATCAATTGTCTGACGtttt                                                                     <  2:1320353/100‑1 (MQ=255)
                     cgATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGtttt                                                                     <  1:1496019/100‑1 (MQ=255)
                      gATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTg                                                                    >  2:822158/1‑100 (MQ=255)
                       aTCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGa                                                                   <  1:145163/100‑1 (MQ=255)
                       aTCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGa                                                                   <  1:315402/100‑1 (MQ=255)
                         ccATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATg                                                                 <  2:726510/100‑1 (MQ=255)
                          cATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGt                                                                >  2:1394833/1‑100 (MQ=255)
                           aTTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGtt                                                               <  1:981187/100‑1 (MQ=255)
                           aTTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGtt                                                               <  2:1106451/100‑1 (MQ=255)
                            ttGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTc                                                              <  1:603138/100‑1 (MQ=255)
                             tGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATACAACTTACCGATCCATTGTCTGACGTTTTGATGtt                                                               >  2:1402554/1‑98 (MQ=255)
                              gcggcgAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTc                                                              >  2:1427569/1‑98 (MQ=255)
                                 gcgAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCg                                                         <  2:819093/100‑1 (MQ=255)
                                 gcgAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCg                                                         <  1:193925/100‑1 (MQ=255)
                                     cgccTTTTTCCCTATCGCCCAACAAGAACACCGGCACGTTTTCTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCgg                                                        <  2:1245816/94‑1 (MQ=255)
                                      ggCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGt                                                    >  1:895180/1‑100 (MQ=255)
                                        cTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTc                                                  >  2:3510/1‑100 (MQ=255)
                                              cccGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGTCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTg                                            >  2:841380/1‑100 (MQ=255)
                                                 gATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATa                                         <  1:1179458/100‑1 (MQ=255)
                                                  aTCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAg                                        <  1:1053177/100‑1 (MQ=255)
                                                     gCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTg                                     >  1:246139/1‑100 (MQ=255)
                                                      cccAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGa                                    <  2:449133/100‑1 (MQ=255)
                                                        cAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAAc                                  <  1:1233771/100‑1 (MQ=255)
                                                        cAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAAc                                  <  1:1257588/100‑1 (MQ=255)
                                                        cAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAAc                                  >  2:457111/1‑100 (MQ=255)
                                                         aaCAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACa                                 <  1:1244226/100‑1 (MQ=255)
                                                            aGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCa                              <  1:963228/100‑1 (MQ=255)
                                                             ggAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAg                             >  1:500932/1‑100 (MQ=255)
                                                             ggAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAg                             >  1:686044/1‑100 (MQ=255)
                                                             ggAAGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAg                             >  2:749153/1‑100 (MQ=255)
                                                               aaGACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGc                           <  2:191358/100‑1 (MQ=255)
                                                                 gACCGGCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAg                         <  2:1128802/100‑1 (MQ=255)
                                                                     ggCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCaa                     >  1:259085/1‑100 (MQ=255)
                                                                     ggCACGTTTTGTTGGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCaa                     >  1:1544781/1‑100 (MQ=255)
                                                                     ggCACGTTATGTTGGCGCGCACGAAACCTACCGATCAAGAGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGAAg                         >  2:763363/1‑96 (MQ=255)
                                                                       cACGTTTTGTTGGCGCTTATGAAACTTACCGCTCTATTGGCTGACGTTTTGATTTTCGTCCGGATGTTCCATTTGATAGCTGAACAGCAGGCAGTCAATg                   <  1:1015926/100‑1 (MQ=255)
                                                                             ttgttgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCg             <  1:1233010/100‑1 (MQ=255)
                                                                              tgttgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGt            <  1:285603/100‑1 (MQ=255)
                                                                                atctcgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGttt          <  2:1363163/96‑1 (MQ=255)
                                                                                 tgGCGCTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTg         <  2:686042/100‑1 (MQ=255)
                                                                                   gcgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGaa       <  1:510022/100‑1 (MQ=255)
                                                                                    cgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGtttagat      >  1:1363170/1‑96 (MQ=255)
                                                                                    cgcTCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAag      <  1:317430/100‑1 (MQ=255)
                                                                                      cTCATGAAACTTACCGATCAATTGTCTGATGCTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTCAACATCAGGCAGTCAATGGCTTCGTTTGAagag    <  2:950283/100‑1 (MQ=255)
                                                                                       tCATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAagaga   <  1:822163/100‑1 (MQ=255)
                                                                                        cATGAAACTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAagagag  >  1:1446400/1‑100 (MQ=255)
                                                                                              |                                                                                             
TCGACAAGCTCCAGCAGGTCGCGATCCATTGCGGCGAGGGCTTTTTCCCGATCGCCCAACAGGAAGACCGGCACGTTTTGTTGGCGCTCATGAAGCTTACCGATCAATTGTCTGACGTTTTGATGTTCGTCCGGATGTTCCATTTGATAGCTGAACATCAGGCAGTCAATGGCTTCGTTTGAAGAGAG  >  NC_000913/4340193‑4340380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A