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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,184,522 C→T 37.7% V107I (GTC→ATC)  gspC ← general secretory pathway component, cryptic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,184,5220CT37.7% 110.6 / 125.1 114V107I (GTC→ATC) gspCgeneral secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base C (39/32);  new base T (19/24);  total (58/56)
Fisher's exact test for biased strand distribution p-value = 3.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01

Only 100 of 116 total aligned reads displayed.

CCCGGCGCTGACTCAAGGGCTTCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTAGGTGTTTCCT  >  W3110S.gb/4184455‑4184590
                                                                   |                                                                    
cccGGCGCTGACTCAAGGGCTTCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACaa                                                                    >  1:4267047/1‑70 (MQ=255)
      gcTGACTCAAGGGCTTCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGt                                                             >  1:1598864/1‑71 (MQ=255)
         gACTCAAGGGCTTCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGtct                                                           >  1:4957873/1‑70 (MQ=255)
                gggCTTCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTc                                                   <  1:1583698/71‑1 (MQ=255)
                  gCTTCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGa                                                 <  1:593225/71‑1 (MQ=255)
                  gCTTCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGa                                                 >  1:3873427/1‑71 (MQ=255)
                    ttCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGAc                                                                      <  1:4039789/48‑1 (MQ=255)
                    ttCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGAc                                                                      <  1:752582/48‑1 (MQ=255)
                      cGTTGAGGGAGTATCGCTTTTGTTCTCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGAtgt                                              <  1:1603012/70‑1 (MQ=255)
                      cGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGAtgt                                              >  1:4590866/1‑70 (MQ=255)
                      cGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACaa                                                                    >  1:4118454/1‑48 (MQ=255)
                      cGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACaa                                                                    >  1:3068837/1‑48 (MQ=255)
                      cGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACaa                                                                    >  1:3096046/1‑48 (MQ=255)
                      cGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACaa                                                                    >  1:1767083/1‑48 (MQ=255)
                      cGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGAtgt                                              <  1:831902/70‑1 (MQ=255)
                       gTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGAtgt                                              <  1:2699357/69‑1 (MQ=255)
                        ttGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCtcat                                                        <  1:935842/58‑1 (MQ=255)
                        ttGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAg                                           >  1:3087697/1‑71 (MQ=255)
                        ttGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAg                                           >  1:2666621/1‑71 (MQ=255)
                        ttGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAg                                           <  1:1907239/71‑1 (MQ=255)
                         tGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAg                                           >  1:4494336/1‑70 (MQ=255)
                         tGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAg                                           >  1:4626297/1‑70 (MQ=255)
                          gAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGAt                                                >  1:5027457/1‑64 (MQ=255)
                           aGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTAc                                        <  1:459347/71‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGATaa                                                                    <  1:3767908/37‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACa                                                                     <  1:3836132/36‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTcatcat                                                     <  1:291735/52‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCg                                                  <  1:4076645/55‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCg                                                  <  1:2670205/55‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCg                                                  <  1:2991187/55‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCg                                                  <  1:2020079/55‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATg                                    >  1:3724665/1‑69 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGcc                                  <  1:4006652/71‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGcc                                  <  1:4004499/71‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGc                                   <  1:3284285/70‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGc                                   <  1:711453/70‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGc                                   <  1:2215209/70‑1 (MQ=255)
                                 tATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGc                                   >  1:461336/1‑70 (MQ=255)
                                   tCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCa                                 >  1:5086930/1‑70 (MQ=255)
                                   tCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCAt                                >  1:3434866/1‑71 (MQ=255)
                                   tCGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCAt                                <  1:780042/71‑1 (MQ=255)
                                   tCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCtcat                                                        <  1:4531934/47‑1 (MQ=255)
                                   tCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGa                                                 >  1:5112245/1‑54 (MQ=255)
                                   tCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGAt                                                >  1:363982/1‑55 (MQ=255)
                                   tCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCAt                                >  1:4175800/1‑71 (MQ=255)
                                    cGCTTTTGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACaa                                      >  1:2984520/1‑64 (MQ=255)
                                     gCTTTTGTTCGCTCCCCTCATTAATTAAGACAAaagaa                                                               >  1:1156412/1‑38 (MQ=255)
                                     gCTTTTGTTCGCTCCCCTCATTAATTAAGACAAaagaa                                                               >  1:2084334/1‑38 (MQ=255)
                                     gCTTTTGTTCGCTCCCCTCATTAATTAAGACAAaagaa                                                               >  1:3792962/1‑38 (MQ=255)
                                     gCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCAtt                               >  1:2607316/1‑70 (MQ=255)
                                     gCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCAtt                               >  1:4254174/1‑70 (MQ=255)
                                     gCTTTTATTCGCTCCCCTCATTAATTAAGACAAaagaa                                                               >  1:141905/1‑38 (MQ=255)
                                       ttttGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGa                                            >  1:1003616/1‑55 (MQ=255)
                                       ttttGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGa                                            >  1:1275801/1‑55 (MQ=255)
                                         ttGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGAtgt                                              <  1:2685648/51‑1 (MQ=255)
                                         ttGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAg                            <  1:3168979/69‑1 (MQ=255)
                                          tGTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGAtgt                                              <  1:2142769/50‑1 (MQ=255)
                                          tGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTaa                             >  1:2594572/1‑67 (MQ=255)
                                           gTTCGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTAc                                        <  1:2305510/55‑1 (MQ=255)
                                           gTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgcgc                         <  1:908516/70‑1 (MQ=255)
                                              cGCTCCCCTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCtat                      <  1:2765779/70‑1 (MQ=255)
                                               gCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCtata                     <  1:219855/70‑1 (MQ=255)
                                                   cccTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCtat                      <  1:3861347/65‑1 (MQ=255)
                                                   cccTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgc                           <  1:2582153/60‑1 (MQ=255)
                                                   cccTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgc                           <  1:1744177/60‑1 (MQ=255)
                                                    ccTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgcgc                         <  1:3367217/61‑1 (MQ=255)
                                                    ccTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgcgc                         <  1:2369760/61‑1 (MQ=255)
                                                     cTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgctc                         <  1:2920320/60‑3 (MQ=255)
                                                     cTCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCt                        <  1:921086/61‑1 (MQ=255)
                                                     cTCATTAATTAAGACAAAAGAAGTCTCATCATTCGAtgt                                              <  1:811946/39‑1 (MQ=255)
                                                     cTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCAt                                <  1:4636569/53‑1 (MQ=255)
                                                     cTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgcgc                         >  1:1055013/1‑60 (MQ=255)
                                                     cTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgcgc                         >  1:1120001/1‑60 (MQ=255)
                                                     cTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgcgc                         >  1:2411019/1‑60 (MQ=255)
                                                     cTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgcgc                         >  1:1845585/1‑60 (MQ=255)
                                                     cTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCt              <  1:237484/71‑1 (MQ=255)
                                                      tCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGc                                   <  1:4173397/49‑1 (MQ=255)
                                                      tCATTAATTAAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCta                       >  1:1901192/1‑61 (MQ=255)
                                                       cATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGGGCta                       >  1:1311320/1‑60 (MQ=255)
                                                        attaattaAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTa            >  1:1914813/1‑70 (MQ=255)
                                                        attaattaAGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTAg           >  1:52312/1‑71 (MQ=255)
                                                        attaattaAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTAg           >  1:1284935/1‑71 (MQ=255)
                                                        attaattaAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTAg           >  1:3108216/1‑71 (MQ=255)
                                                         ttaattaaGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGc                                   <  1:4920847/46‑1 (MQ=255)
                                                         ttaattaaGACAAAAGAAGTCTCATCATTCGATGTGAGGACAATGc                                   <  1:958788/46‑1 (MQ=255)
                                                          taattaaGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCtata                     <  1:4544772/59‑1 (MQ=255)
                                                           aattaaGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCa                                 >  1:4007555/1‑46 (MQ=255)
                                                           aattaaGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCa                                 >  1:3648255/1‑46 (MQ=255)
                                                           aattaaGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCtata                     <  1:4177451/58‑1 (MQ=255)
                                                           aattaaGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTAGgtg        >  1:2249784/1‑71 (MQ=255)
                                                             ttaaGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCa                                 <  1:3686111/44‑1 (MQ=255)
                                                             ttaaGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCa                                 <  1:3198371/44‑1 (MQ=255)
                                                             ttaaGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCtat                      <  1:3107122/55‑1 (MQ=255)
                                                             ttaaGACAAAAGAAGTCTCATCATTCGATGTGAGTACa                                       <  1:69315/38‑1 (MQ=255)
                                                               aaGACAAAAGAAGTCTCATCATTCGATGTGAGTACAAt                                     >  1:1702532/1‑38 (MQ=255)
                                                               aaGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTAGGTGTTTc    >  1:109086/1‑71 (MQ=255)
                                                                aGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCtat                      >  1:3021974/1‑52 (MQ=255)
                                                                aGATAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTAGGTGTTTc    <  1:2375127/70‑1 (MQ=255)
                                                                aGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAgcgc                         <  1:74173/49‑1 (MQ=255)
                                                                  aCAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTGTAGAGAGCTTAGGTGTTTCCt  >  1:2818704/1‑70 (MQ=255)
                                                                   |                                                                    
CCCGGCGCTGACTCAAGGGCTTCGTTGAGGGAGTATCGCTTTTGTTCGCTCCCCTCATTAATTAAGACAAAAGAAGTCTCATCATTCGATGTGAGTACAATGCCATTAAGCGCTATAGAGAGCTTAGGTGTTTCCT  >  W3110S.gb/4184455‑4184590

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