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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,983,818 A→G 17.3% V144A (GTG→GCG)  yqeF ← predicted acyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,983,8180AG17.3% 241.7 / 43.2 104V144A (GTG→GCG) yqeFpredicted acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (53/33);  new base G (11/7);  total (64/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.04e-01

Only 100 of 111 total aligned reads displayed.

TCGCGAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACATGTGGTGC  >  W3110S.gb/2983749‑2983888
                                                                     |                                                                      
  gcgAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACaa                                                                     <  1:242674/71‑1 (MQ=255)
   cgAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAg                                                                    <  1:2101353/71‑1 (MQ=255)
        cAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACaa                                                                     >  1:2051603/1‑65 (MQ=255)
         aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGt                                                               >  1:3640228/1‑70 (MQ=255)
         aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGt                                                               >  1:3652152/1‑70 (MQ=255)
         aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              <  1:3158304/71‑1 (MQ=255)
         aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              <  1:668137/71‑1 (MQ=255)
         aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              <  1:1216594/71‑1 (MQ=255)
         aGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              <  1:1211314/71‑1 (MQ=255)
           aTTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaa                                                            >  1:1606698/1‑71 (MQ=255)
             tttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaac                                                           >  1:2649923/1‑70 (MQ=255)
             tttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              >  1:1960068/1‑67 (MQ=255)
             tttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              >  1:3371030/1‑67 (MQ=255)
             tttCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              >  1:4217504/1‑67 (MQ=255)
               tCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGa                                                                   <  1:2364988/60‑1 (MQ=255)
                cggcggTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaaccaac                                                       >  1:3477293/1‑71 (MQ=255)
                 ggcggTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGcaca                                                                      >  1:917461/1‑55 (MQ=255)
                     gTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGc                                                   <  1:171545/70‑1 (MQ=255)
                       gACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACaa                                                                     >  1:1530368/1‑50 (MQ=255)
                       gACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                                >  1:4572231/1‑71 (MQ=255)
                       gACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                                >  1:1430659/1‑71 (MQ=255)
                        acacCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACaa                                                                     <  1:4588041/49‑1 (MQ=255)
                        acacCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAtt                                               >  1:1846723/1‑71 (MQ=255)
                        acacCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAtt                                               >  1:2919571/1‑71 (MQ=255)
                          acCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGAGCAAGa                                                                   >  1:1095778/1‑49 (MQ=255)
                           ccAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaacca                                                         <  1:1432582/58‑1 (MQ=255)
                             aaTATGATAATCATTGAAGGCATCCCACAACCCATCATGCACaa                                                                     >  1:3417690/1‑44 (MQ=255)
                               tatGATAATCATTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTc                                                              <  1:3680570/49‑1 (MQ=255)
                               tatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              <  1:2134161/49‑1 (MQ=255)
                               tatGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTa                                                 <  1:2359410/62‑1 (MQ=255)
                                 tGATAATCATTGAAGGCATCCCACAACCCATCATGca                                                                        >  1:1091949/1‑37 (MQ=255)
                                 tGATAATCATTGAAGGCATCCCACAACCCATCATGca                                                                        >  1:2339131/1‑37 (MQ=255)
                                 tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTc                                                              >  1:3539268/1‑47 (MQ=255)
                                 tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                      >  1:4207138/1‑71 (MQ=255)
                                 tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                      <  1:3735881/71‑1 (MQ=255)
                                 tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCt                                       <  1:2201151/70‑1 (MQ=255)
                                 tGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCt                                       <  1:452520/70‑1 (MQ=255)
                                    tAATCATTGAAGGCATCCAACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                                >  1:2329266/1‑58 (MQ=255)
                                       tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTcaacc                                                          <  1:2812903/45‑1 (MQ=255)
                                       tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGcc                                            <  1:3627148/59‑1 (MQ=255)
                                       tCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAcc                                <  1:1519548/71‑1 (MQ=255)
                                        cATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTa                                                 >  1:2988129/1‑53 (MQ=255)
                                        cATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTa                                                 >  1:249996/1‑53 (MQ=255)
                                         aTTGAAGGCATCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCgg                              >  1:161028/1‑71 (MQ=255)
                                          ttGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGt                             >  1:344316/1‑71 (MQ=255)
                                               ggCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGc                        >  1:2221122/1‑71 (MQ=255)
                                                  aTCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAt                     <  1:4493252/71‑1 (MQ=255)
                                                   tCCCACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtc                    <  1:122465/71‑1 (MQ=255)
                                                   tCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGc                                             <  1:2429197/46‑1 (MQ=255)
                                                    cccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAt                     >  1:118005/1‑69 (MQ=255)
                                                     ccACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTa                                                 >  1:2272558/1‑40 (MQ=255)
                                                     ccACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGcc                                            >  1:2741674/1‑45 (MQ=255)
                                                     ccACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGcc                                            >  1:2169480/1‑45 (MQ=255)
                                                     ccACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtca                   <  1:1571562/70‑1 (MQ=255)
                                                     ccACAACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtca                   <  1:3874910/70‑1 (MQ=255)
                                                     ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTa                                                 >  1:3095586/1‑40 (MQ=255)
                                                     ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                                >  1:1718379/1‑41 (MQ=255)
                                                     ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTAt                                                >  1:2221035/1‑41 (MQ=255)
                                                     ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag                  >  1:3379077/1‑71 (MQ=255)
                                                     ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag                  >  1:3437016/1‑71 (MQ=255)
                                                     ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag                  >  1:4336855/1‑71 (MQ=255)
                                                     ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcag                  >  1:2691329/1‑71 (MQ=255)
                                                     ccACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCAAGGCTGTGCACCGGTGCGGCTAtcag                  >  1:4280192/1‑71 (MQ=255)
                                                     ccACAACCCATCATGCACAACACTGTCAACCAACTGGCTATTGCCAAGCTGTGc                                   >  1:77691/1‑54 (MQ=255)
                                                     ccACAACACATCATGCGCAAGACTGTCAACCAACTGGc                                                   >  1:876685/1‑38 (MQ=38)
                                                     acacaACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGcc                                            >  1:4309935/2‑45 (MQ=255)
                                                       acaACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagtc                <  1:3392266/71‑1 (MQ=255)
                                                        caACCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCa                                           <  1:4007133/43‑1 (MQ=255)
                                                         aaCCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTg                            >  1:3277626/1‑57 (MQ=255)
                                                         aaCCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagt                 >  1:38640/1‑68 (MQ=255)
                                                          aCCCATCATGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagtcag              >  1:3547547/1‑70 (MQ=255)
                                                          aCCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtcagtcag              >  1:12271/1‑70 (MQ=255)
                                                          aCCCATCATCCACAACACTGTCAACCAACTCGCTATTGCCAAGCtgt                                     >  1:1251127/1‑47 (MQ=255)
                                                            ccATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGaa            >  1:3615912/1‑70 (MQ=255)
                                                            ccATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAAc           <  1:1861271/71‑1 (MQ=255)
                                                             catcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCtg                                      <  1:3431128/43‑1 (MQ=255)
                                                             catcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAc                                 >  1:1504793/1‑48 (MQ=255)
                                                             catcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAc                                 >  1:1864109/1‑48 (MQ=255)
                                                             catcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAc                                 >  1:4371319/1‑48 (MQ=255)
                                                             catcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCAc                                 >  1:1900519/1‑48 (MQ=255)
                                                              atcatGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAt         >  1:1729770/1‑71 (MQ=255)
                                                               tcatGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCa                                  >  1:1125548/1‑45 (MQ=255)
                                                               tcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCt                                       <  1:368229/40‑1 (MQ=255)
                                                               tcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtg        <  1:2819595/71‑1 (MQ=255)
                                                               tcatGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAt         <  1:3983482/70‑1 (MQ=255)
                                                                 atGCGCAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg      >  1:3694270/1‑71 (MQ=255)
                                                                 atGCACAAGACTGTCGACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCgg                         >  1:2607907/1‑52 (MQ=255)
                                                                 atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGc                                        >  1:904285/1‑37 (MQ=255)
                                                                 atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGc                           >  1:1854217/1‑50 (MQ=255)
                                                                 atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCg                          >  1:2470942/1‑51 (MQ=255)
                                                                 atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtca                   >  1:1749151/1‑58 (MQ=255)
                                                                 atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAAc           >  1:4060992/1‑66 (MQ=255)
                                                                 atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtgtg      >  1:864119/1‑71 (MQ=255)
                                                                 atGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACAtg        <  1:38802/69‑1 (MQ=255)
                                                                 atGCACAAGACTGTCAACCAAATGGCTATTGCCAAGCTGTGCACCGGGGCGGCTATCAGTCAGAACAtg        <  1:1401986/69‑1 (MQ=255)
                                                                 atGCACAAGAATGTCAACCAACTGGATATTGCCAAga                                        >  1:4310900/1‑36 (MQ=37)
                                                                   gCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTAtc                    <  1:113661/55‑1 (MQ=255)
                                                                    cacaAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCgg                              >  1:921025/1‑44 (MQ=255)
                                                                    cacaAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACATgtggtg   >  1:869296/1‑71 (MQ=255)
                                                                     acaAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACATGTGGTgc  >  1:873712/1‑71 (MQ=255)
                                                                     |                                                                      
TCGCGAGCCAGATTTTCGGCGGTGACACCAATATGATAATCATTGAAGGCATCCCACAACCCATCATGCACAAGACTGTCAACCAACTGGCTATTGCCAAGCTGTGCACCGGTGCGGCTATCAGTCAGAACATGTGGTGC  >  W3110S.gb/2983749‑2983888

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