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 F212 I1 R1 174 80.0 3892211 96.7% 3763768 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,017,924 G→A D198N (GAC→AAC)  rmuC → DNA recombination protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,017,9240GA95.3% 207.7 / ‑1.3 64D198N (GAC→AAC) rmuCDNA recombination protein
Reads supporting (aligned to +/- strand):  ref base G (2/1);  new base A (32/29);  total (34/30)
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

AGAACGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCGACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTCA  >  NC_000913/4017827‑4018020
                                                                                                 |                                                                                                
aGAACGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAAc                                                                                                <  1:1146104/100‑1 (MQ=255)
   aCGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAAt                                                                                             >  2:91102/1‑100 (MQ=255)
    cGCCATACCCTGACCCACGAAATTCGCAATCTCCGGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATa                                                                                            >  1:794808/1‑100 (MQ=255)
     gCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATaa                                                                                           >  1:1176641/1‑100 (MQ=255)
       cATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATaaaa                                                                                         <  2:1158171/100‑1 (MQ=255)
        atccccTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAAc                                                                                        <  2:1090724/97‑1 (MQ=255)
        aTACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCGACAATAAAAc                                                                                        <  2:1440138/100‑1 (MQ=255)
        aTACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAAc                                                                                        <  1:819191/100‑1 (MQ=255)
        aTACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAAc                                                                                        <  2:656833/100‑1 (MQ=255)
         tACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAAca                                                                                       <  2:963564/100‑2 (MQ=255)
           cccTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCa                                                                                     >  2:1655284/1‑100 (MQ=255)
             cTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAgg                                                                                   <  2:445196/100‑1 (MQ=255)
              tGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAggg                                                                                  >  1:932891/1‑100 (MQ=255)
               gACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGc                                                                                 <  1:1758218/100‑1 (MQ=255)
               gACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGc                                                                                 >  1:60448/1‑100 (MQ=255)
                aCCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCa                                                                                >  2:1092044/1‑100 (MQ=255)
                  ccACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAAc                                                                              >  2:73208/1‑100 (MQ=255)
                   cACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACt                                                                             >  2:844493/1‑100 (MQ=255)
                   cACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACt                                                                             >  2:141056/1‑100 (MQ=255)
                   cACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACt                                                                             >  1:666497/1‑100 (MQ=255)
                   cACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAACGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGACAGGCGACAATAAAACCCAGGGCAAc                                                                              >  1:858560/1‑99 (MQ=255)
                     cGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTgg                                                                           >  1:1511910/1‑100 (MQ=255)
                       aaaTTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTgggg                                                                         <  2:254777/100‑1 (MQ=255)
                       aaaTTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTgggg                                                                         <  2:1227464/100‑1 (MQ=255)
                       aaaTTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTgggg                                                                         >  2:745655/1‑100 (MQ=255)
                          ttCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGa                                                                      >  1:827382/1‑100 (MQ=255)
                           tCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACATGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGa                                                                      >  1:372703/1‑99 (MQ=255)
                               aaTCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGgtag                                                                 <  2:564334/100‑1 (MQ=255)
                                aTCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGgtagt                                                                <  1:1087879/100‑1 (MQ=255)
                                    ccAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTg                                                            >  1:555368/1‑100 (MQ=255)
                                    ccAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTg                                                            <  1:1761250/100‑1 (MQ=255)
                                    ccAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTg                                                            >  1:133490/1‑100 (MQ=255)
                                          aCTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCgg                                                      >  1:1870143/1‑100 (MQ=255)
                                          aCTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCgg                                                      >  1:1872051/1‑100 (MQ=255)
                                                 gcgcAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTgg                                               <  1:1090948/100‑1 (MQ=255)
                                                   gcAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAg                                             <  2:137900/100‑1 (MQ=255)
                                                   gcAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAg                                             <  2:1922609/100‑1 (MQ=255)
                                                   gcAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAg                                             <  2:50414/100‑1 (MQ=255)
                                                   gcAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAg                                             <  1:1259139/100‑1 (MQ=255)
                                                    cAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAgg                                            <  1:1832308/100‑1 (MQ=255)
                                                    cAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAgg                                            <  2:210601/100‑1 (MQ=255)
                                                    cAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAgg                                            <  1:165844/100‑1 (MQ=255)
                                                     aaaGGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGc                                           <  2:1041464/100‑1 (MQ=255)
                                                               ggAAGCGATCAACCTGACGCGCGCGCTGAAAGGCGACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTg                                 >  1:472596/1‑100 (MQ=255)
                                                                  aGCGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGt                              <  2:370205/100‑1 (MQ=255)
                                                                    cGATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGa                            >  1:1254038/1‑100 (MQ=255)
                                                                     gATCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGaa                           >  1:1616657/1‑100 (MQ=255)
                                                                      aTCAACCTGACGGGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAg                          <  2:28798/100‑1 (MQ=255)
                                                                      aTCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCAAGCGCAACTGGGGCGAGGTAGTATTGACGCGGGTGATGGAGGCGTCCGGTcg                                  >  1:1903786/1‑91 (MQ=255)
                                                                       tCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAgg                         <  1:91102/100‑1 (MQ=255)
                                                                       tCAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAgg                         >  2:436357/1‑100 (MQ=255)
                                                                        cAACCTGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAggg                        <  2:1248845/100‑1 (MQ=255)
                                                                             tGACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatga                   >  2:724232/1‑100 (MQ=255)
                                                                              gACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaa                  <  1:328322/100‑1 (MQ=255)
                                                                              gACGCGCGCGCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaa                  <  2:1008363/100‑1 (MQ=255)
                                                                                cgcgcgcgCTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaata                >  2:1560195/1‑100 (MQ=255)
                                                                                  cgcgcgcTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGtatgaatatg              <  1:329274/100‑1 (MQ=255)
                                                                                        cTGAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAAccc        >  1:599997/1‑100 (MQ=255)
                                                                                          gAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAg      >  2:467868/1‑100 (MQ=255)
                                                                                          gAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAg      >  2:865566/1‑100 (MQ=255)
                                                                                          gAAAGGCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAg      >  1:1000575/1‑100 (MQ=255)
                                                                                              ggCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTCa  >  1:1629424/1‑100 (MQ=255)
                                                                                              ggCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTCa  >  2:83611/1‑100 (MQ=255)
                                                                                              ggCAACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCCGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTCa  >  2:348395/1‑100 (MQ=255)
                                                                                                 |                                                                                                
AGAACGCCATACCCTGACCCACGAAATTCGCAATCTCCAGCAACTCAACGCGCAAATGGCCCAGGAAGCGATCAACCTGACGCGCGCGCTGAAAGGCGACAATAAAACCCAGGGCAACTGGGGCGAGGTAGTATTGACGCGGGTGCTGGAGGCTTCCGGTCTGCGTGAAGGGTATGAATATGAAACCCAGGTCA  >  NC_000913/4017827‑4018020

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A