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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 980,278 C→T 28.3% V9V (GTG→GTA)  cspI ← cold shock protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE980,2780CT28.3% 197.2 / 82.1 120V9V (GTG→GTA) cspIcold shock protein
Reads supporting (aligned to +/- strand):  ref base C (43/43);  new base T (17/17);  total (60/60)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 122 total aligned reads displayed.

CAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTCC  >  minE/980211‑980348
                                                                   |                                                                      
 aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa                                                                    <  1:5510559/71‑1 (MQ=255)
 aaaCACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa                                                                    <  1:720516/71‑1 (MQ=255)
 aaaCACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACt                                                                     >  1:5153911/1‑70 (MQ=255)
 aaaCACATCTTTACTACCATCAACAGGAGAAATAAAGCCGAAACCTTTATCAGCGTTAAACCATTTTACt                                                                     >  1:5127617/1‑70 (MQ=255)
   acacATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTAcga                                                                    >  1:1052620/1‑67 (MQ=9)
   acacATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTAcga                                                                    >  1:4621677/1‑67 (MQ=9)
    cacaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTc                                                                        >  1:1156252/1‑64 (MQ=255)
    cacaTCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAAc                                                                 <  1:1513145/71‑1 (MQ=255)
         cTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCa                                                               >  1:5511648/1‑68 (MQ=255)
           ttGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGt                                                             >  1:3644293/1‑68 (MQ=255)
            tgctgcCATCATCAGGAGTGATAAAGCCAAAACCTTTATCTGCGTTAAACCATTTTACTAAAc                                                                 >  1:4022803/1‑63 (MQ=9)
             gctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtt                                                         <  1:4479250/70‑1 (MQ=255)
              gagcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAttt                                                        <  1:3892167/68‑1 (MQ=255)
              gagcCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAttt                                                        <  1:82126/68‑1 (MQ=255)
              ctgcCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAttt                                                        <  1:1591862/70‑1 (MQ=255)
                 ccATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                                     <  1:4351269/70‑1 (MQ=255)
                   aTCTTTCGGTGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa                                                                    <  1:3328034/53‑1 (MQ=255)
                   aTCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTa                                                                    <  1:160521/53‑1 (MQ=255)
                      tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa                                                   >  1:5261761/1‑67 (MQ=255)
                      tttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACa                                               >  1:1425652/1‑71 (MQ=255)
                       ttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACa                                               >  1:4028751/1‑70 (MQ=255)
                       ttCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACa                                               >  1:2488971/1‑70 (MQ=255)
                        tCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACAt                                              >  1:2333624/1‑70 (MQ=255)
                           gagTGATGAAGCCGAAGCCTTTGTCAGCGTTGAGCCATTTTACGATACCAGTCAtt                                                         >  1:3514997/3‑56 (MQ=255)
                           gagTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtt                                                         >  1:1857598/3‑56 (MQ=255)
                           gagTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtt                                                         >  1:4568935/3‑56 (MQ=255)
                             gTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatta                                         >  1:2103233/1‑70 (MQ=255)
                              tgatgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCTCTAAACCAGTCATTTTGTTAGACATAatta                                         <  1:4387484/69‑1 (MQ=255)
                                atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAttt                                                        <  1:3203337/52‑1 (MQ=255)
                                atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                                     <  1:210327/55‑1 (MQ=255)
                                atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                                     <  1:5633836/55‑1 (MQ=255)
                                atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                                     <  1:8492/55‑1 (MQ=255)
                                atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                                     <  1:4986770/55‑1 (MQ=255)
                                atgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                                     <  1:4753505/55‑1 (MQ=255)
                                 tgaAGCCGAAGCCTTTGTCAGCGTTGAACCATTTTACGATACCAGTCAtt                                                         >  1:899380/1‑50 (MQ=255)
                                 tgaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAat                                           >  1:2128480/1‑64 (MQ=255)
                                  gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTg                                                      >  1:2865127/1‑52 (MQ=255)
                                  gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTg                                                      >  1:4645415/1‑52 (MQ=255)
                                  gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt                                          <  1:4098546/64‑1 (MQ=255)
                                  gaAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAatt                                          <  1:1845520/64‑1 (MQ=255)
                                   aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAATCCAGTCATTTTGTTAGACATAATTATTAc                                     >  1:3841039/1‑68 (MQ=255)
                                   aaaCCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCtt                                  >  1:923052/1‑71 (MQ=255)
                                      ccAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               <  1:2256864/71‑1 (MQ=255)
                                      ccAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTc                                                            >  1:1237644/1‑42 (MQ=25)
                                      ccAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCa                                                           >  1:3179028/1‑43 (MQ=25)
                                      ccAAAACCTTTATCTGCGTTAAACCATTTTACTAAACCAGTCa                                                           >  1:1923790/1‑43 (MQ=25)
                                       cAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCAtttt                                                       >  1:5024372/1‑46 (MQ=255)
                                       cAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               >  1:2594071/1‑70 (MQ=255)
                                        aaaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGt                                                     >  1:5375720/1‑47 (MQ=255)
                                        aaaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               >  1:3169106/1‑69 (MQ=255)
                                        aaaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               >  1:2074788/1‑69 (MQ=255)
                                        aaaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               >  1:490479/1‑69 (MQ=255)
                                        aaaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               >  1:5448399/1‑69 (MQ=255)
                                        aaaaCCTTTTTCAGGGTTAAACCATTTCACTAAACAAGTCATTTTGt                                                     >  1:2076230/1‑47 (MQ=255)
                                        aaaaCCTTTATCTGCGTTAAACCATTTTACTAAACCAGt                                                             <  1:4281685/39‑1 (MQ=25)
                                         aaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTa                                                   >  1:2629414/1‑48 (MQ=255)
                                         aaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               >  1:3407416/1‑68 (MQ=255)
                                         aaaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               >  1:3166722/1‑68 (MQ=255)
                                          aaCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaaga                           <  1:405913/71‑1 (MQ=255)
                                          aaCCTTTATCAGCGTTAAACCATTTTACTAAACCa                                                               >  1:1012348/1‑35 (MQ=25)
                                          aaCCTTTATCAGCGTTAAACCATTTTACTAAACCa                                                               >  1:1136215/1‑35 (MQ=25)
                                           aCCTTTTTCAGGGTTAAACCATTTCACTATACCAGTCATTTTGt                                                     <  1:5152605/44‑1 (MQ=255)
                                           aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAattat                                        >  1:2418489/1‑57 (MQ=255)
                                           aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaagaa                          <  1:5581304/71‑1 (MQ=255)
                                           aCCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaagaa                          <  1:2837519/71‑1 (MQ=255)
                                             cTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAt                        <  1:2764800/71‑1 (MQ=255)
                                              tttgtCAGCGTTGAACCATTTTACGATACCAGTCAttt                                                        <  1:2054396/38‑1 (MQ=12)
                                              tttgtCAGCGTTGAACCATTTTACGATACCAGTCAttt                                                        <  1:4874612/38‑1 (MQ=12)
                                              tttgtCAGCGTTGAACCATTTTACGATACCAGTCAttt                                                        <  1:5566213/38‑1 (MQ=12)
                                              tttatCAGCGTTAAACCATTTTACTAAACGAGTCAttt                                                        <  1:447067/38‑1 (MQ=21)
                                              tttatCAGCGTTAAACCATTTTACTAAACCAGTCAttt                                                        <  1:5506022/38‑1 (MQ=25)
                                              tttatCAGCGTTAAACCATTTTACTAAACCAGTCAttt                                                        <  1:2365632/38‑1 (MQ=25)
                                              tttatCAGCGTTAAACCATTTTACTAAACCAGTCATTTTATTTGa                                                 <  1:1796779/45‑1 (MQ=255)
                                                tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAtt                       <  1:2627508/69‑1 (MQ=255)
                                                tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAAtt                       <  1:4040715/69‑1 (MQ=255)
                                                tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTa                      <  1:5659966/70‑1 (MQ=255)
                                                tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTa                      <  1:165492/70‑1 (MQ=255)
                                                tttCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAg                     >  1:697425/1‑71 (MQ=255)
                                                  tCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGc                    <  1:1376651/70‑1 (MQ=255)
                                                  tCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGc                    <  1:2869713/70‑1 (MQ=255)
                                                  tCAGCGTTAAACCATTTTACTAAACCAGTCATTTTAttt                                                   <  1:3098439/39‑2 (MQ=25)
                                                   cAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGc                    <  1:778949/69‑1 (MQ=255)
                                                    aGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCt                 <  1:1923509/71‑1 (MQ=255)
                                                        ttAAACCATTTTACTAAACCAGTCATTTTATTTGa                                                 <  1:5405127/35‑1 (MQ=25)
                                                        ttAAACCATTTTACTAAACCAGTCATTTTATTAGACAt                                              <  1:3734753/38‑1 (MQ=38)
                                                        ttAAACCATTTTACTAAACCAGTCATTTTATTAGACAt                                              <  1:26667/38‑1 (MQ=38)
                                                        ttAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAat                                           <  1:2705755/41‑1 (MQ=255)
                                                          aaaCCATTTTACTAAACCAGTCATTTTATTAGACATat                                            >  1:208707/1‑37 (MQ=37)
                                                          aaaCCATTTTACTAAACCAGTCATTTTATTAGACATAtttta                                        >  1:4194764/1‑40 (MQ=37)
                                                           aaCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAg          <  1:5210032/71‑1 (MQ=255)
                                                           aaCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAg          <  1:1135570/71‑1 (MQ=255)
                                                            aCCATTTCACTAAACCAGTCATTTTGTTAGACATAatta                                         >  1:3903845/1‑39 (MQ=255)
                                                            aCCATTTCACTAAACCAGTCATTTTGTTAGACATAatta                                         >  1:3855462/1‑39 (MQ=255)
                                                            aCCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTg               <  1:5656010/65‑1 (MQ=255)
                                                             ccATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTg               >  1:5586187/1‑64 (MQ=255)
                                                                tttCACTAAACCAGTCATTTTGTTAGACATAatta                                         >  1:1317535/1‑35 (MQ=255)
                                                                tttCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTgaagaa                          <  1:805918/50‑1 (MQ=255)
                                                                  tCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTg                               <  1:930345/43‑1 (MQ=255)
                                                                  tCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGaaa                         >  1:1662990/1‑49 (MQ=255)
                                                                   cACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTcc  >  1:2260131/1‑71 (MQ=255)
                                                                   |                                                                      
CAAACACATCTTTGCTGCCATCTTTCGGCGTGATGAAACCAAAACCTTTTTCAGGGTTAAACCATTTCACTAAACCAGTCATTTTGTTAGACATAATTATTACCTTTTGAAGAAATTAGCCCTTGGGCAGAATGGTCC  >  minE/980211‑980348

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