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 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,012,950 A→G 13.8% V255A (GTG→GCG)  yqeC ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,012,9500AG13.8% 70.3 / 5.3 29V255A (GTG→GCG) yqeCconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (15/10);  new base G (2/2);  total (17/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

GTGAAAATATTCATACCAACCTCAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGTGTTGTTG  >  W3110S.gb/3012882‑3013020
                                                                    |                                                                      
gtgAAAATATTCATACCAACCTCAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTcac                                                                       >  1:3919858/1‑70 (MQ=255)
 tgAAAATATTCATACCAACCTCAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTcaca                                                                      <  1:3073817/70‑1 (MQ=255)
   aaaaTATTCATACCAACCTCAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTCACAAAt                                                                   >  1:3594076/1‑71 (MQ=255)
     aaTATTCATACCAACCTCAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTCACAAATCt                                                                 <  1:2575125/71‑1 (MQ=255)
                cAACCTCAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTg                                                      <  1:1348383/71‑1 (MQ=255)
                 aaCCTCAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTCACAAATCTg                                                                >  1:2717104/1‑60 (MQ=255)
                      cAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGAt                                                >  1:1585398/1‑71 (MQ=255)
                                ccTTTCAGTAACCCGGAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTg                                         <  1:2885721/68‑1 (MQ=255)
                                       gTAACACGGAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGccc                               <  1:3149361/71‑1 (MQ=255)
                                            ccGGAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCccagcc                           <  1:2682439/70‑1 (MQ=255)
                                            ccGGAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCccagc                            >  1:3958888/1‑69 (MQ=255)
                                              ggAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCccagc                            >  1:2785296/1‑67 (MQ=255)
                                               gAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGc                                                     <  1:3115685/41‑1 (MQ=255)
                                               gAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCccagc                            >  1:1929956/1‑66 (MQ=255)
                                                 aTACCCGGGCCGCTAATTCGCAAATCTGCGCGCGATTGCAGGATGTTCtt                                          >  1:702516/1‑50 (MQ=255)
                                                    cccGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCtt                                          >  1:1494867/1‑47 (MQ=255)
                                                    cccGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCct                  >  1:3267688/1‑71 (MQ=255)
                                                        ggCCGCTAATTCGCAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCg                                  >  1:1366888/1‑51 (MQ=255)
                                                           cGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTg                                         <  1:618200/41‑1 (MQ=255)
                                                            gCTAATTCGCAAATCTGCGCGCGATTGCAGGATGt                                              <  1:1197831/35‑1 (MQ=255)
                                                            gCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCcca                              >  1:4148101/1‑51 (MQ=255)
                                                            gCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTAcgtcg          >  1:757835/1‑71 (MQ=255)
                                                            gCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTAcgtcg          >  1:3859383/1‑71 (MQ=255)
                                                            gCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTAcgtcg          >  1:1702554/1‑71 (MQ=255)
                                                            gCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTAcgtc           >  1:118965/1‑70 (MQ=255)
                                                             cTAATTCACAATTCTGCGCGCGATTGCAGGATGTTCTTg                                         <  1:687751/39‑1 (MQ=255)
                                                                aTTCGCAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGccc                               <  1:2486605/46‑1 (MQ=255)
                                                                aTTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGcc                   <  1:4529048/58‑1 (MQ=255)
                                                                aTTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGtgtt      >  1:818496/1‑71 (MQ=255)
                                                                 ttCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCctc                 <  1:3065675/59‑1 (MQ=255)
                                                                 ttCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGtgttg     >  1:64167/1‑71 (MQ=255)
                                                                   cacaAATCTGCGCGCGATTGCGGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGTgttgtt   >  1:832087/1‑71 (MQ=255)
                                                                   cacaAATCTGCGCGCGATTGCAGGATGTTCTTGtat                                      >  1:545206/1‑36 (MQ=255)
                                                                   cacaAATCTGCGCGCGATTGCAGGATGTTCTTGtat                                      >  1:1466362/1‑36 (MQ=255)
                                                                   cacaAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTAcgtcg          <  1:2203902/64‑1 (MQ=255)
                                                                   cacaAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGtgttgt    <  1:3859330/70‑1 (MQ=255)
                                                                   cacaAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGtgttgt    <  1:3553499/70‑1 (MQ=255)
                                                                   cacaAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGTgttgtt   >  1:1684578/1‑71 (MQ=255)
                                                                   cacaAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGTgttgtt   >  1:2551992/1‑71 (MQ=255)
                                                                    acaAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGTGttgttg  <  1:3553881/71‑1 (MQ=255)
                                                                    |                                                                      
GTGAAAATATTCATACCAACCTCAATGGATATCCTTTCAGTAACCCGGAATACCCGGGCCGCTAATTCACAAATCTGCGCGCGATTGCAGGATGTTCTTGTATATCGCCCAGCCAGATTGCCTCTACGTCGTGTTGTTG  >  W3110S.gb/3012882‑3013020

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