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
A1 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 594,454 T→C 29.2% K71K (AAA→AAG)  cusR ← DNA‑binding response regulator in two‑component regulatory system with CusS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb594,4540TC29.2% 103.7 / 56.3 72K71K (AAA→AAG) cusRDNA‑binding response regulator in two‑component regulatory system with CusS
Reads supporting (aligned to +/- strand):  ref base T (28/23);  new base C (6/15);  total (34/38)
Fisher's exact test for biased strand distribution p-value = 6.80e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.22e-01

CCCAACTCCAGCCCCTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCATAATATCGAGGA  >  W3110S.gb/594386‑594521
                                                                    |                                                                   
cccAACTCCAGCCCCTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCttt                                                                   <  1:3129275/71‑1 (MQ=255)
 ccAACTCCAGCCCCTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTa                                                                  <  1:3860675/71‑1 (MQ=255)
 ccAACTCCAGCCCCTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTa                                                                  <  1:1774397/71‑1 (MQ=255)
          gCCCCTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATAGGCATCCCTTTATTGGCGGAg                                                         >  1:4476252/1‑71 (MQ=255)
             ccTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCg                                                       >  1:1013216/1‑70 (MQ=255)
              cTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTa                                                     <  1:1388746/71‑1 (MQ=255)
              cTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTa                                                     <  1:1277756/71‑1 (MQ=255)
                tGACGCGATGTTCAATGGTGCCAAGCTCGGTAAGCAACAGAATCGGCATACCTTTATTGGCGGAGCg                                                       >  1:712568/1‑67 (MQ=255)
                 gACGCGATGTTCAATGGTGCCAAGCGTGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACa                                                  >  1:2905294/1‑71 (MQ=255)
                 gACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTaa                                                    <  1:1762425/69‑1 (MQ=255)
                 gACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGt                                                      <  1:1442783/67‑1 (MQ=255)
                  aCGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACAt                                                 <  1:153209/71‑1 (MQ=255)
                    gcgATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCgg                                                           <  1:2228494/59‑1 (MQ=255)
                      gATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATgcgc                                             <  1:4135656/71‑1 (MQ=255)
                        tGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCAc                                           <  1:3107969/71‑1 (MQ=255)
                         gTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCAc                                           >  1:2609733/1‑70 (MQ=255)
                          ttCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCgg                                                           >  1:2778647/1‑53 (MQ=255)
                          ttCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACg                                          <  1:2646887/70‑1 (MQ=255)
                          ttCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACg                                          <  1:4369192/70‑1 (MQ=255)
                          ttCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATg                                                <  1:2291468/64‑1 (MQ=255)
                          ttCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGa                                         >  1:4365382/1‑71 (MQ=255)
                          ttCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCATTTATTGGCgg                                                           >  1:4354537/1‑53 (MQ=255)
                           tCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGa                                         >  1:848009/1‑70 (MQ=255)
                            cAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATgcg                                              >  1:1745217/1‑64 (MQ=255)
                            cAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGata                                       >  1:570766/1‑71 (MQ=255)
                            cAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGata                                       >  1:2677212/1‑71 (MQ=255)
                            cAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGata                                       >  1:4050137/1‑71 (MQ=255)
                             aaTGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGata                                       <  1:371327/70‑1 (MQ=255)
                             aaTGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTa                                                     <  1:2810850/56‑1 (MQ=255)
                              aTGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCg                                                            <  1:3656915/48‑1 (MQ=255)
                              aTGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCg                                                            <  1:2108937/48‑1 (MQ=255)
                               tGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCgg                                                           <  1:3828497/48‑1 (MQ=255)
                               tGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATcc                                    <  1:2143493/71‑1 (MQ=255)
                                 gTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGATATCCCa                                  <  1:2542683/71‑1 (MQ=255)
                                  tGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAg                                 <  1:1927719/71‑1 (MQ=255)
                                    ccAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGc                                <  1:3454753/70‑1 (MQ=255)
                                     cAAGCGCTGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCg                              <  1:1473714/71‑1 (MQ=255)
                                     cAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCg                              >  1:2140384/1‑71 (MQ=255)
                                      aaGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTa                                                     >  1:524688/1‑47 (MQ=255)
                                      aaGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGt                             >  1:1211817/1‑71 (MQ=255)
                                      aaGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGGACGATATCCCAGCCGt                             >  1:1395827/1‑71 (MQ=255)
                                      aaGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGat                                        >  1:2803555/1‑60 (MQ=255)
                                       aGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGtt                            <  1:246827/71‑1 (MQ=255)
                                       aGCGCGGTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGtt                            <  1:569304/71‑1 (MQ=255)
                                         agcgGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCa                          <  1:4254296/70‑1 (MQ=255)
                                             gTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTa                                                     >  1:1106814/1‑40 (MQ=255)
                                             gTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGt                       <  1:3525339/70‑1 (MQ=255)
                                             gTAAGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTc                      <  1:2825381/71‑1 (MQ=255)
                                               aaGCAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGa                                         >  1:1062739/1‑50 (MQ=255)
                                                aGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTaa                                                    >  1:4506381/1‑38 (MQ=255)
                                                aGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTc                      >  1:3561536/1‑68 (MQ=255)
                                                aGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTc                      >  1:874539/1‑68 (MQ=255)
                                                  cAACAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGgca                 <  1:2617719/71‑1 (MQ=255)
                                                   aaCAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATc                                     >  1:2436160/1‑50 (MQ=255)
                                                     cAGAATCGGCATCCCCTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGgcag                >  1:3678590/1‑69 (MQ=255)
                                                      aGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCat             <  1:2843939/71‑1 (MQ=255)
                                                      aGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCat             <  1:3539981/71‑1 (MQ=255)
                                                       gAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCat             <  1:2527122/70‑1 (MQ=255)
                                                        aaTCGGCATCCCCTTATTGGCGGTGCGTAACATgcgc                                             <  1:3380329/37‑1 (MQ=38)
                                                        aaTCGGCATCCCCTTATTGGCGGAGCGTAACATgcgc                                             <  1:2471263/37‑1 (MQ=255)
                                                            ggCATCCCTTTATTGGCGGAGCGTAACATGCGCACGata                                       >  1:842840/1‑39 (MQ=255)
                                                             gCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCATAATATCg      <  1:517791/71‑1 (MQ=255)
                                                             gCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCATAATATCg      <  1:2055859/71‑1 (MQ=255)
                                                               aTCCCTTTATTGGCGGAGCGTAACATGCGCACGata                                       >  1:3500648/1‑36 (MQ=255)
                                                               aTCCCTTTATTGGCGGAGCGTAACATGCGCACGata                                       >  1:1392483/1‑36 (MQ=255)
                                                               aTCCCTTTATTGGCGGAGCGTAACATGCGCACGat                                        >  1:2457563/1‑35 (MQ=255)
                                                               aTCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCATAATATCGAg    <  1:896021/71‑1 (MQ=255)
                                                                tCCCCTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGtt                            <  1:26536/46‑1 (MQ=255)
                                                                 ccccTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCATAATATCGAGGa  >  1:3563172/1‑71 (MQ=255)
                                                                  ccTTTATTGGCGGAGCGTAACATGCGCACGATATCCCa                                  >  1:3111450/1‑38 (MQ=255)
                                                                   cTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCa                          >  1:480324/1‑45 (MQ=255)
                                                                   cTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCa                          >  1:1313969/1‑45 (MQ=255)
                                                                   cTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTc                      >  1:1854576/1‑49 (MQ=255)
                                                                   cTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTc                      >  1:3264868/1‑49 (MQ=255)
                                                                    tttATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTcc                     <  1:928/49‑1 (MQ=255)
                                                                    |                                                                   
CCCAACTCCAGCCCCTTGACGCGATGTTCAATGGTGCCAAGCGCGGTAAGCAACAGAATCGGCATCCCTTTATTGGCGGAGCGTAACATGCGCACGATATCCCAGCCGTTCACGTCCGGCAGCATAATATCGAGGA  >  W3110S.gb/594386‑594521

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