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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,788,749 C→T 31.8% P38S (CCG→TCG)  ygaF → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,788,7490CT31.8% 24.7 / 15.3 22P38S (CCG→TCG) ygaFhypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (6/9);  new base T (4/3);  total (10/12)
Fisher's exact test for biased strand distribution p-value = 6.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01

CCGCCATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTAC  >  W3110S.gb/2788684‑2788805
                                                                 |                                                        
ccGCCATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGcc                                                     >  1:2890674/1‑71 (MQ=255)
ccGCCATGCAACAGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGcc                                                     >  1:2182678/1‑71 (MQ=255)
 cGCCATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGCCt                                                    >  1:2096021/1‑71 (MQ=255)
   ccATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGt                                                  <  1:3362340/71‑1 (MQ=255)
   ccATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGt                                                  <  1:2471956/71‑1 (MQ=255)
        cAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGcccc                                                         >  1:3392847/1‑59 (MQ=255)
        cAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCAc                                               >  1:1127333/1‑69 (MQ=255)
        cAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCAc                                               >  1:3648358/1‑69 (MQ=255)
             gattgatGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACgg                                        >  1:1953647/1‑71 (MQ=255)
               ttgatGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGccc                                                          >  1:2070931/1‑51 (MQ=255)
               ttgatGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGccc                                                          >  1:2644439/1‑51 (MQ=255)
               ttgatGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGccc                                                          >  1:3129137/1‑51 (MQ=255)
               ttgatGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGCCt                                                    <  1:1931668/57‑1 (MQ=255)
                         tCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAg                              >  1:2695249/1‑69 (MQ=255)
                                 cccGCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATc                    <  1:3839579/71‑1 (MQ=255)
                                   cGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCa                  >  1:2445320/1‑71 (MQ=255)
                                    gCATTGCGTTGCTGGAAAAAGAGTCCGCCTCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCAt                 >  1:2329673/1‑71 (MQ=255)
                                    gCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGa                                           >  1:29189/1‑45 (MQ=255)
                                     cATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCAc                                               <  1:893668/40‑1 (MQ=255)
                                              gCTGGAAAAAGAGTCCGCCTCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTc        <  1:1257698/70‑1 (MQ=255)
                                               cTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCt       <  1:1067423/70‑1 (MQ=255)
                                                  gAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCcaca                                  <  1:1900089/40‑1 (MQ=255)
                                                  gAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTAt     <  1:266142/69‑1 (MQ=255)
                                                  gAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTAt     <  1:1579536/69‑1 (MQ=255)
                                                  gAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTa   <  1:3695366/71‑1 (MQ=255)
                                                   aaaaaGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTac  <  1:25458/71‑1 (MQ=255)
                                                                 |                                                        
CCGCCATGCAACTGATTGATGTCTATCCGGACGCCCGCATTGCGTTGCTGGAAAAAGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTAC  >  W3110S.gb/2788684‑2788805

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A