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
A5 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,294,438 T→C 11.9% L395S (TTG→TCG)  yraM → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,294,4380TC11.9% 146.5 / 12.5 59L395S (TTG→TCG) yraMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (28/24);  new base C (5/2);  total (33/26)
Fisher's exact test for biased strand distribution p-value = 4.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01

AAGCCAGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAATATCGAAAATCGCGT  >  W3110S.gb/3294370‑3294504
                                                                    |                                                                  
aaGCCAGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGc                                                                  >  1:3746401/1‑71 (MQ=255)
 aGCCAGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGtt                                                                    <  1:3640576/68‑1 (MQ=255)
 aGCCAGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGtt                                                                    <  1:196578/68‑1 (MQ=255)
    cAGGTTCAGCAGGATGGCGCGAGTTTTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGaa                                                              <  1:2993395/71‑1 (MQ=255)
    cAGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGGTGaa                                                              <  1:5264/71‑1 (MQ=255)
    cAGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGaa                                                              <  1:96759/71‑1 (MQ=255)
    cAGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTCGCTGaa                                                              <  1:2049727/71‑1 (MQ=255)
     aGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAag                                                             <  1:1428363/71‑1 (MQ=255)
      ggTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGaa                                                              >  1:1667632/1‑69 (MQ=255)
       gTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAagag                                                           >  1:2435886/1‑71 (MQ=255)
        ttCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGc                                                          <  1:1824555/71‑1 (MQ=255)
        ttCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTCGCTGAAGAGc                                                          <  1:1882524/71‑1 (MQ=255)
             cagGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGc                                                                  >  1:3239278/1‑58 (MQ=255)
              agGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACt                                                    >  1:1346874/1‑71 (MQ=255)
              agGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTCGCTGAAGAGCAACACt                                                    >  1:1826305/1‑71 (MQ=255)
               ggATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTc                                                   <  1:3500066/71‑1 (MQ=255)
                  tGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGc                                                >  1:527204/1‑71 (MQ=255)
                  tGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTCGCTGaa                                                              >  1:2972201/1‑57 (MQ=255)
                  tGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTCGCTGAAGAGCaa                                                        >  1:4231753/1‑63 (MQ=255)
                  tGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGGTGAAGAGTTGCTGAAGAGCAACACTCCGc                                                >  1:3763275/1‑71 (MQ=255)
                        gAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACg                                          <  1:3883283/71‑1 (MQ=255)
                          gTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCaa                                                        >  1:165409/1‑55 (MQ=255)
                          gTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTa                                        >  1:207743/1‑71 (MQ=255)
                             ttGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGaa                                                              >  1:2127455/1‑46 (MQ=255)
                             ttGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGaa                                                              >  1:11537/1‑46 (MQ=255)
                             ttGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGc                                                <  1:1543844/60‑1 (MQ=255)
                             ttGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTCGCTGAAGAGCAACACTCCGCTGAACGTACTg                                     >  1:2650557/1‑71 (MQ=255)
                              tgtgGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTg                                     <  1:2856101/70‑1 (MQ=255)
                               gtgGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTg                                                                   <  1:4190508/39‑1 (MQ=255)
                               gtgGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGaa                                                              >  1:2005857/1‑44 (MQ=255)
                               gtgGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAag                                                             >  1:1055475/1‑45 (MQ=255)
                                 ggtcggtcCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCAc                                 >  1:1049212/1‑71 (MQ=255)
                                   tcggtcCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTg                               <  1:2732871/71‑1 (MQ=255)
                                       tcCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAAc                            >  1:2111931/1‑70 (MQ=255)
                                        ccGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAaca                                                      >  1:936759/1‑43 (MQ=255)
                                         cGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAg                         <  1:1356811/71‑1 (MQ=255)
                                         cGTTGCTGAAAAATAACGTTGAAGAGTCGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAg                         >  1:582793/1‑71 (MQ=255)
                                           ttGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGcc                       >  1:849564/1‑71 (MQ=255)
                                           ttGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGACACTGAACCAGc                        >  1:2468068/1‑70 (MQ=255)
                                             gCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACt                                >  1:410627/1‑60 (MQ=255)
                                             gCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCg                      >  1:183856/1‑70 (MQ=255)
                                             gCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCg                      >  1:2608355/1‑70 (MQ=255)
                                                gAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGc                                   <  1:1236069/54‑1 (MQ=255)
                                                 aaaaaTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGgag                   <  1:2780933/69‑1 (MQ=255)
                                                 aaaaaTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGgag                   <  1:549712/69‑1 (MQ=255)
                                                 aaaaaTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGgag                   <  1:1781379/69‑1 (MQ=255)
                                                 aaaaaTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGaa                 >  1:3514662/1‑71 (MQ=255)
                                                 aaaaaTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGaa                 >  1:372755/1‑71 (MQ=255)
                                                  aaaaTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAat                <  1:4259024/71‑1 (MQ=255)
                                                   aaaTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAata               <  1:2936480/71‑1 (MQ=255)
                                                   aaaTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAata               >  1:3486914/1‑71 (MQ=255)
                                                     aTAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGaa                             >  1:3534939/1‑55 (MQ=255)
                                                      tAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAATATCg            <  1:638072/71‑1 (MQ=255)
                                                        aCGTTGAAGAGTTGCTTAAGAGCAACACTCCGCTGAACGTACTGGc                                   <  1:4023714/46‑1 (MQ=255)
                                                        aCGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGc                                   <  1:4026084/46‑1 (MQ=255)
                                                        aCGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGc                                   <  1:1029210/46‑1 (MQ=255)
                                                          gTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAATATCGaaaa        <  1:3573895/71‑1 (MQ=255)
                                                             gAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAATATCGaaa         <  1:108393/67‑1 (MQ=255)
                                                             gAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAATATCGAAAATcg     >  1:4142767/1‑71 (MQ=255)
                                                                gagTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAATATCGAAAATCGCGt  >  1:540566/1‑71 (MQ=255)
                                                                 agTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACt                                >  1:239702/1‑40 (MQ=255)
                                                                    |                                                                  
AAGCCAGGTTCAGCAGGATGGCGCGAGTATTGTGGTCGGTCCGTTGCTGAAAAATAACGTTGAAGAGTTGCTGAAGAGCAACACTCCGCTGAACGTACTGGCACTGAACCAGCCGGAGAATATCGAAAATCGCGT  >  W3110S.gb/3294370‑3294504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A