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
A23 F74 I1 R1 13 20.1 450294 97.3% 438136 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,373,525 G→T A84E (GCA→GAA)  pbuG ← Guanine/hypoxanthine permease PbuG

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,373,5250GT94.7% 55.1 / ‑5.8 19A84E (GCA→GAA) pbuGGuanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base T (10/8);  total (11/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTT  >  USA300TCH1516_ALE/2373393‑2373659
                                                                                                                                    |                                                                                                                                      
cTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCa                                                                                                                                >  1:29494/1‑141 (MQ=255)
                 tAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCAGGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTAt                                                                                                               <  1:82516/141‑1 (MQ=255)
                 tAATATCGCAAAGAATATACCTGAGAACAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTAt                                                                                                               <  2:15299/141‑1 (MQ=255)
                   atatCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTa                                                                                                             >  1:1554/1‑141 (MQ=255)
                          aaaGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCTAt                                                                                                      >  1:169979/1‑141 (MQ=255)
                               atatACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATa                                                                                                 <  2:129175/141‑1 (MQ=255)
                               atatACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATa                                                                                                 <  2:25906/141‑1 (MQ=255)
                                tataCCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAg                                                                                                <  1:33110/141‑1 (MQ=255)
                                                              aaCTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGc                                                                  <  1:182440/141‑1 (MQ=255)
                                                                 ttGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTAc                                                               >  2:167551/1‑141 (MQ=255)
                                                                               ccATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCtt                                                 >  2:219418/1‑141 (MQ=255)
                                                                                         cacaACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCAtttt                                       <  1:77500/141‑1 (MQ=255)
                                                                                                             aTGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCtt                   >  1:6765/1‑141 (MQ=255)
                                                                                                             aTGCATTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCtt                   >  2:71324/1‑141 (MQ=255)
                                                                                                                 aTTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAac               >  1:16816/1‑141 (MQ=255)
                                                                                                                 aTTTAATCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAac               >  1:87709/1‑141 (MQ=255)
                                                                                                                      aTCCCATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTg          <  2:169979/141‑1 (MQ=255)
                                                                                                                         ccATACCTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTa       >  2:50977/1‑141 (MQ=255)
                                                                                                                              ccTGGTTCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACtt  >  1:147719/1‑141 (MQ=255)
                                                                                                                                    |                                                                                                                                      
CTAAACCCTGTGACGGTTAATATCGCAAAGAATATACCTGAGAATAAAACGCCTGTTAAACCAACTTGCCAAGGAATACCCATGGTTAACACAACAGTAAATGCAAAGAATGCATTTAATCCCATACCTGGTGCTAACGCAATTGGATATTTAGCTATTAGCCCCATGAATAGCGAGCCTACAAATGCTGCTAATGCAGTCGCTACAAAAATGGCACCTTGGTCCATTTTCATATCTTCTGATACGCCTTTAACACCTGCTAAACTT  >  USA300TCH1516_ALE/2373393‑2373659

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