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 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,566,303 T→C 100% C8C (TGT→TGC)  yihR → predicted aldose‑1‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,566,3030TC80.6% 128.5 / 24.0 57C8C (TGT→TGC) yihRpredicted aldose‑1‑epimerase
Reads supporting (aligned to +/- strand):  ref base T (11/0);  new base C (29/16);  total (40/17)
Fisher's exact test for biased strand distribution p-value = 2.35e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.24e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCAGTTTTTGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTGCCGCGGGGGATTAT  >  W3110S.gb/3566241‑3566363
                                                              |                                                            
gCAGTTTTTGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCaa                                                        <  1:2775984/69‑1 (MQ=255)
gCAGTTTTTGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCaa                                                        <  1:2244228/69‑1 (MQ=255)
      tttGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCAcc                                                  >  1:3285020/1‑69 (MQ=255)
      tttGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCAcc                                                  >  1:3310210/1‑69 (MQ=255)
      tttGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCAcc                                                  >  1:1850914/1‑69 (MQ=255)
      tttGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCAcc                                                  >  1:1929354/1‑69 (MQ=255)
      tttGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCAcc                                                  >  1:749811/1‑69 (MQ=255)
      tttGGGTTTGACATCAGCCTAACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCAcc                                                  >  1:3093679/1‑69 (MQ=255)
           gTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCaa                                                >  1:2522032/1‑66 (MQ=255)
           gTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAata                                              <  1:236189/68‑1 (MQ=255)
           gTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAata                                              <  1:3397208/68‑1 (MQ=255)
            tttGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATg                                            <  1:2358564/69‑1 (MQ=255)
            tttGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATg                                            <  1:3386783/69‑1 (MQ=255)
                    cAGCCTCACTGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAg                                    <  1:1398996/69‑1 (MQ=255)
                     aGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGTATGCa                                                         >  1:3214062/1‑47 (MQ=255)
                     aGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGTATGCa                                                         >  1:2778476/1‑47 (MQ=255)
                     aGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAg                                    >  1:3171426/1‑68 (MQ=255)
                     aGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAg                                    >  1:3635437/1‑68 (MQ=255)
                     aGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAg                                    >  1:1703263/1‑68 (MQ=255)
                         tCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGa                                <  1:1899528/68‑1 (MQ=255)
                         tCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGa                                <  1:776941/68‑1 (MQ=255)
                           aCGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAg                             >  1:1115834/1‑69 (MQ=255)
                           aCGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAg                             >  1:2141569/1‑69 (MQ=255)
                           aCGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAg                             >  1:1442854/1‑69 (MQ=255)
                           aCGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAg                             >  1:2189883/1‑69 (MQ=255)
                             gggAGGCTGTATGTCGTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGAc                           >  1:2958876/1‑69 (MQ=255)
                             gggAGGCTGTATGTCGTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGAc                           >  1:469091/1‑69 (MQ=255)
                                aGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGt                        >  1:2902307/1‑69 (MQ=255)
                                aGGCTGTATGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGt                        >  1:2906663/1‑69 (MQ=255)
                                       aTGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACtt                 >  1:3298554/1‑69 (MQ=255)
                                       aTGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACtt                 >  1:974147/1‑69 (MQ=255)
                                       aTGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACtt                 >  1:2830971/1‑69 (MQ=255)
                                       aTGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACtt                 >  1:2866488/1‑69 (MQ=255)
                                       aTGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACtt                 >  1:2880063/1‑69 (MQ=255)
                                        tGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCaa                                                >  1:686188/1‑37 (MQ=255)
                                        tGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGc                                      >  1:3207882/1‑47 (MQ=255)
                                        tGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGc                                      >  1:811133/1‑47 (MQ=255)
                                        tGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGc                                      >  1:3008518/1‑47 (MQ=255)
                                        tGTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGc                                      >  1:674072/1‑47 (MQ=255)
                                         gTCGTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTg                >  1:2643362/1‑68 (MQ=255)
                                         gTCGTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTg                >  1:3672988/1‑68 (MQ=255)
                                         gTCGTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTg                >  1:636298/1‑68 (MQ=255)
                                         gTCGTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTGc               >  1:2962518/1‑69 (MQ=255)
                                         gTCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACt                  <  1:3597669/66‑1 (MQ=255)
                                          tCGTTAATTAAGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTGcc              >  1:3155195/1‑69 (MQ=255)
                                            gTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGt                        >  1:763475/1‑57 (MQ=255)
                                            gTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGt                        >  1:38500/1‑57 (MQ=255)
                                              taattaaGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTGCcgcg           <  1:1950836/68‑1 (MQ=255)
                                               aattaaGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACa                              <  1:311899/48‑1 (MQ=255)
                                               aattaaGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACa                              <  1:392979/48‑1 (MQ=255)
                                               aattaaGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGttt                      >  1:1147755/1‑56 (MQ=255)
                                               aattaaGGTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGttt                      >  1:1074846/1‑56 (MQ=255)
                                               aattaaGGTGCCTTGAATGCAAATCACCAATATGCATTGCAGTGGACa                              <  1:243581/48‑1 (MQ=255)
                                               aattaaGCTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACa                              <  1:299526/48‑1 (MQ=38)
                                                   aaGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTGCCGCGGGGGAt     >  1:210061/1‑69 (MQ=255)
                                                      gTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTGCCGCGGGGGATTAt  <  1:2740943/69‑1 (MQ=255)
                                                      gTGCCTTGCATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTGCCGCGGGGGATTAt  <  1:3252529/69‑1 (MQ=255)
                                                              |                                                            
GCAGTTTTTGGGTTTGACATCAGCCTCACGGGAGGCTGTATGTCGTTAATTAAGGTGCCTTGTATGCAAATCACCAATATGCATTGCAGTGGACAGACCGTTTCACTTGCCGCGGGGGATTAT  >  W3110S.gb/3566241‑3566363

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A