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
A1 F2 I200 R1 216 30.8 1683622 97.2% 1636480 87.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,717,498 G→C G374A (GGC→GCC)  ydhK → FUSC family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,717,4980GC92.0% 72.4 / 0.3 25G374A (GGC→GCC) ydhKFUSC family protein
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base C (10/13);  total (10/15)
Fisher's exact test for biased strand distribution p-value = 5.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

ACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGC  >  NZ_CP009273/1717416‑1717585
                                                                                  |                                                                                       
aCATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATgg                                                                                  <  2:118907/90‑1 (MQ=255)
 cATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGAACATTTTGTACGTTGATGATGATTGCCGCATGGa                                                                                 >  2:666756/1‑90 (MQ=255)
      ggCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTAtt                                                                            <  2:470459/90‑1 (MQ=255)
        ccTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGc                                                                          <  2:292895/90‑1 (MQ=255)
         cTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCt                                                                         >  2:285915/1‑90 (MQ=255)
                    tACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGa                                                              <  2:418268/90‑1 (MQ=255)
                          tAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCgg                                                        >  1:98825/1‑90 (MQ=255)
                                cGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCaa                                                  >  2:643514/1‑90 (MQ=255)
                                cGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCaa                                                  <  2:591513/90‑1 (MQ=255)
                                                gggCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGgca                                  >  1:514556/1‑90 (MQ=255)
                                                 ggCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGgcag                                 >  2:310528/1‑90 (MQ=255)
                                                         aCATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGc                         <  1:784942/90‑1 (MQ=255)
                                                         aCATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGc                         <  1:310528/90‑1 (MQ=255)
                                                           aTTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTg                       <  1:796275/90‑1 (MQ=255)
                                                           aTTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTg                       <  1:80939/90‑1 (MQ=255)
                                                             tttGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCg                     <  1:180191/90‑1 (MQ=255)
                                                                gTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGtac                  <  2:217489/90‑1 (MQ=255)
                                                                    gTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTg                       <  2:217286/81‑1 (MQ=255)
                                                                    gTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTg                       >  1:217286/1‑81 (MQ=255)
                                                                    gTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGtactcta              >  1:706339/1‑90 (MQ=255)
                                                                    gTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGtactcta              >  2:659316/1‑90 (MQ=255)
                                                                      tgatgatgaTTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGtactctact            >  1:829972/1‑90 (MQ=255)
                                                                           atgatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTccgcc       <  2:415668/90‑1 (MQ=255)
                                                                           atgatTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTccgcc       <  1:393786/90‑1 (MQ=255)
                                                                                tGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCgc  <  2:450967/90‑1 (MQ=255)
                                                                                  |                                                                                       
ACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGC  >  NZ_CP009273/1717416‑1717585

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: 

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC  >  NZ_CP009273/1717400‑1717590
                                                                                                  |                                                                                            
TACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCC                                                                                             >  SRR3722079.295305/1‑100 (MQ=60)
TACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCC                                                                                             >  SRR3722079.692344/1‑100 (MQ=60)
                                GTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGG                                                             >  SRR3722079.99607/1‑100 (MQ=60)
                                                      TATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCA                                       >  SRR3722079.519263/1‑100 (MQ=60)
                                                                         ACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCT                    <  SRR3722079.793361/100‑1 (MQ=60)
                                                                         ACATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCT                    <  SRR3722079.313054/100‑1 (MQ=60)
                                                                          CATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTA                   >  SRR3722079.219137/1‑100 (MQ=60)
                                                                          CATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTA                   >  SRR3722079.713830/1‑100 (MQ=60)
                                                                           ATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTAC                  <  SRR3722079.804813/100‑1 (MQ=60)
                                                                           ATTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTAC                  <  SRR3722079.81595/100‑1 (MQ=60)
                                                                            TTTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACT                 >  SRR3722079.838854/1‑100 (MQ=60)
                                                                             TTTGTACGTTGATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTC                <  SRR3722079.181766/100‑1 (MQ=60)
                                                                                       GATGATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCA      >  SRR3722079.536979/1‑100 (MQ=60)
                                                                                           agagacaGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC  <  SRR3722079.71578/93‑1 (MQ=60)
                                                                                           ATGATTGCCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC  <  SRR3722079.397068/100‑1 (MQ=60)
                                                                                                  |                                                                                            
TACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTATGTGGAGCGGGCTGCGTACATTTTGTACGTTGATGATGATTGGCGCATGGAGTATTGCTTCGCAATGGGATGCCGGTGCCAATGCATTAACGCTGGCAGCAATTAGCTGCGTACTCTACTCCGCCGTCGCAGCAC  >  NZ_CP009273/1717400‑1717590

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: