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
A0 F0 I1 R1 715 38.4 1606192 96.6% 1551581 120.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,655,347 C→T *109* (TAG→TAA)  ynfA ← UPF0060 family inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,655,3470CT93.8% 87.2 / ‑1.0 32*109* (TAG→TAA) ynfAUPF0060 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (15/15);  total (16/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.42e-01

ATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATA  >  NC_000913/1655215‑1655475
                                                                                                                                    |                                                                                                                                
aTCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTg                                                                                                                            >  2:427840/1‑139 (MQ=255)
          gCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccagcc                                                                                                                  <  1:169958/139‑5 (MQ=255)
               aGTAATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                            <  2:388052/139‑1 (MQ=255)
                 tGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                          <  2:605656/139‑1 (MQ=255)
                                          gcgcTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCaa                                                                                 >  1:714301/1‑139 (MQ=255)
                                           cgcTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccagcc                                                                                                                  <  2:106544/106‑5 (MQ=255)
                                           cgcTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccagcc                                                                                                                  >  1:106544/1‑102 (MQ=255)
                                                   aTGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCAc                                                                        <  2:34696/139‑1 (MQ=255)
                                                        tGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                   <  2:773802/139‑1 (MQ=255)
                                                          aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGAt                                                                                                     <  2:533615/103‑1 (MQ=255)
                                                          aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                                 >  1:720587/1‑139 (MQ=255)
                                                          aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                                 >  1:778233/1‑139 (MQ=255)
                                                          aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                                 <  2:478326/139‑1 (MQ=255)
                                                          aCAAAAGATGAAATAAAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGAt                                                                                                     >  1:533615/1‑103 (MQ=255)
                                                                gATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATa                                                           <  1:302473/139‑1 (MQ=255)
                                                                 aTGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATaa                                                          >  2:513098/1‑139 (MQ=255)
                                                                           aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCa                                                                                  <  2:733266/106‑1 (MQ=255)
                                                                           aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCa                                                                                  >  1:733266/1‑106 (MQ=255)
                                                                                 tttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGc                                          <  2:778233/139‑1 (MQ=255)
                                                                                   tGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCa                                        >  1:242647/1‑139 (MQ=255)
                                                                                       aGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCca                                    <  2:714301/139‑1 (MQ=255)
                                                                                                  ccTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGc                         <  2:720587/139‑1 (MQ=255)
                                                                                                   ctctTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGcc                        >  2:643880/1‑139 (MQ=255)
                                                                                                            tatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACg               >  1:517568/1‑139 (MQ=255)
                                                                                                             atTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                                     >  1:65835/1‑36 (MQ=255)
                                                                                                             atTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                                     <  2:65835/37‑2 (MQ=255)
                                                                                                             atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGcc                                         <  2:567157/112‑1 (MQ=255)
                                                                                                             atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGcc                                         >  1:567157/1‑112 (MQ=255)
                                                                                                             atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGc              >  1:421722/1‑139 (MQ=255)
                                                                                                             atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGc              >  1:614887/1‑139 (MQ=255)
                                                                                                              ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGcc             >  1:276786/1‑139 (MQ=255)
                                                                                                                         gATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATa  <  1:227057/139‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                
ATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATA  >  NC_000913/1655215‑1655475

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A