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
A7 F28 I1 R1 252 48.5 1661298 98.8% 1641362 138.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,871,832 (G)6→7 coding (1448/1476 nt) cdgI → putative c‑di‑GMP binding protein CdgI

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,871,8261.G94.1% 108.1 / 0.4 34coding (1442/1476 nt)cdgIputative c‑di‑GMP binding protein CdgI
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base G (13/19);  total (14/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.35e-01

CTGACCGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAGCGGCGCAGAGA  >  NC_000913/1871687‑1871954
                                                                                                                                            |                                                                                                                                 
cttaacGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCCGCCGTATTGGCCCGGTTTTTTCAACGGGCGACACGCGTAATCTCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGCAAAGCGa                                                                                                                                    <  2:56778/135‑1 (MQ=255)
cTGACCGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGa                                                                                                                                    <  1:245193/140‑1 (MQ=255)
cTGACCGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGa                                                                                                                                    <  1:49976/140‑1 (MQ=255)
  gACCGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑gg                                                                                                                                <  1:128199/140‑1 (MQ=255)
  gACCGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑gg                                                                                                                                >  2:72365/1‑140 (MQ=255)
    ccGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑gggg                                                                                                                              <  2:229994/140‑1 (MQ=255)
     cGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑ggggg                                                                                                                             >  1:392428/1‑140 (MQ=255)
          ttAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑gggggggcaa                                                                                                                        <  1:544699/140‑5 (MQ=255)
          ttAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑gg                                                                                                                                >  2:431575/1‑132 (MQ=255)
          ttAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑gg                                                                                                                                >  2:496881/1‑132 (MQ=255)
          ttAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑gg                                                                                                                                <  1:431575/132‑1 (MQ=255)
          ttAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑gg                                                                                                                                <  1:496881/132‑1 (MQ=255)
                  aGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGa                                                                                                                 <  2:164901/140‑1 (MQ=255)
                        gatgTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATtc                                                                                                           >  1:668975/1‑140 (MQ=255)
                            ttCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAGGGGGGGGCAACAAAGTGATTATtcatc                                                                                                        >  1:115763/1‑140 (MQ=255)
                              ccTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCata                                                                                                     >  2:238014/1‑140 (MQ=255)
                                  aaCAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAGGGGGGGGCAACAAAGTGATTATTCATCATAttt                                                                                                  <  2:115763/140‑1 (MQ=255)
                                  aaCAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTa                                                                                                 >  2:475054/1‑140 (MQ=255)
                                           ccATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCaaaa                                                                                        <  2:668975/140‑1 (MQ=255)
                                                        cACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCa                                                                           <  1:475054/140‑1 (MQ=255)
                                                           ggTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGc                                                                        >  2:123834/1‑140 (MQ=255)
                                                            gTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCt                                                                       >  2:786479/1‑140 (MQ=255)
                                                                    aaCGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGt                                                               <  1:123834/140‑1 (MQ=255)
                                                                         gTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCtt                                                          <  2:138176/140‑1 (MQ=255)
                                                                         gTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCtt                                                          <  1:72365/140‑1 (MQ=255)
                                                                              acGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCa                                                     <  1:786479/140‑1 (MQ=255)
                                                                                gcgTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATa                                                   >  2:377064/1‑140 (MQ=255)
                                                                                  gTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACa                                                 <  2:166358/140‑1 (MQ=255)
                                                                                  gTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACa                                                 >  2:694879/1‑140 (MQ=255)
                                                                                   tAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCg                                                                <  1:746797/124‑1 (MQ=255)
                                                                                   tAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCg                                                                >  2:746797/1‑124 (MQ=255)
                                                                                          tcGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATttatta                                         >  2:592882/1‑140 (MQ=255)
                                                                                           cGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCttt                                                         <  2:28698/123‑1 (MQ=255)
                                                                                           cGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCttt                                                         >  1:28698/1‑123 (MQ=255)
                                                                                           cGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTtattac                                        >  1:162354/1‑140 (MQ=255)
                                                                                              ttGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTtattactatt                                    >  2:796109/1‑140 (MQ=255)
                                                                                                            gCAGATAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTtc                       <  2:261792/140‑1 (MQ=255)
                                                                                                                aTAAAGCCTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTtcccct                   >  2:210622/1‑140 (MQ=255)
                                                                                                                      ccTTACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAg             <  1:231937/140‑1 (MQ=255)
                                                                                                                        ttACGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAgcg           <  1:210622/140‑1 (MQ=255)
                                                                                                                          aCGCGAAGCGAAAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAgcggc         <  1:694879/140‑1 (MQ=255)
                                                                                                                          aCGCGAAGCGAAAAGCGA‑‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAgcggcg        <  1:796109/140‑1 (MQ=255)
                                                                                                                                agcgaaAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAGCGGCGCagag   <  1:238014/140‑1 (MQ=255)
                                                                                                                                 gcgaaAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAGCGGCGCAgaga  <  1:377064/140‑1 (MQ=255)
                                                                                                                                 gcgaaAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAGCGGCGCAgaga  <  2:340620/140‑1 (MQ=255)
                                                                                                                                 gcgaaAAGCGAG‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAGCGGCGCAgaga  <  2:162354/140‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                 
CTGACCGGCTTTAGTAACAGATATGATGTTCCTGAACAAATGACCATCAGTATTGGCACGGTTTTTTCAACGGGTGACACGCGTAATATCTCGCTTGTCATGACGGAAGCAGATAAAGCCTTACGCGAAGCGAAAAGCGA‑‑GGGGGGCAACAAAGTGATTATTCATCATATTTAAGTGCAAAAATATTCAGAGCCATGCTTTTTGCGTGGCTTTTGCATACAATTTATTACTATTACCCCTAAATTTCCCCTCCCCAGCGGCGCAGAGA  >  NC_000913/1871687‑1871954

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A