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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,497,705 T→G 7.9% R20R (CGT→CGG)  gldA → glycerol dehydrogenase, NAD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,497,7050TG 7.9% 151.1 / 9.5 63R20R (CGT→CGG) gldAglycerol dehydrogenase, NAD
Reads supporting (aligned to +/- strand):  ref base T (36/22);  new base G (2/3);  total (38/25)
Fisher's exact test for biased strand distribution p-value = 3.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

AGCAATTATGGACCGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGTTTTAGGTTTT  >  W3110S.gb/3497639‑3497774
                                                                  |                                                                     
aGCAATTATGGACCGCATTATTCAATCACCGGGTAAATACATCCAGGGAGCTGATGTGATTAATCGTCTgg                                                                   >  1:3124788/1‑71 (MQ=255)
   aaTTATGGACCGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCg                                                                <  1:1492195/71‑1 (MQ=255)
   aaTTATGGACCGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCg                                                                <  1:3115406/71‑1 (MQ=255)
       aTGGACCGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATa                                                            >  1:2104707/1‑71 (MQ=255)
       aTGGACCGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATa                                                            >  1:1479889/1‑71 (MQ=255)
          gACCGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCt                                                         >  1:1632730/1‑71 (MQ=255)
            ccGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTg                                                        >  1:509869/1‑70 (MQ=255)
             cGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGaa                                                      <  1:2465315/71‑1 (MQ=255)
              gCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGGCTGGGCGAATACCTGAAg                                                     >  1:916952/1‑71 (MQ=255)
              gCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGGCTGGGCGAATACCTGAAg                                                     >  1:3224173/1‑71 (MQ=255)
               cATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGa                                                               >  1:2602009/1‑60 (MQ=255)
                attattCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGcc                                                   >  1:2201414/1‑71 (MQ=255)
                   attCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGaa                                                              >  1:1288292/1‑57 (MQ=255)
                   attCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCgat                                                >  1:1489032/1‑69 (MQ=255)
                   attCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCt                                                >  1:157596/1‑71 (MQ=255)
                     tCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTgg                                              >  1:2738928/1‑71 (MQ=255)
                       aaTCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTgg                                              >  1:546323/1‑69 (MQ=255)
                         tCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAg                                           >  1:2835931/1‑70 (MQ=255)
                          cACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGaa                                                              >  1:661925/1‑50 (MQ=255)
                             cGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGc                                      <  1:707801/71‑1 (MQ=255)
                                gTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTgg                                   >  1:2576314/1‑71 (MQ=255)
                                 tAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGt                                  <  1:2655651/71‑1 (MQ=255)
                                 tAAATACATCCAGGGCGCTGATGTGATTAATCGGCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGt                                  <  1:3583212/71‑1 (MQ=255)
                                   aaTACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGt                                  >  1:689796/1‑69 (MQ=255)
                                   aaTACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGt                                  >  1:1372592/1‑69 (MQ=255)
                                      aCATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtg                             >  1:1815463/1‑71 (MQ=255)
                                       cATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtg                             <  1:3146154/70‑1 (MQ=255)
                                       cATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtg                             <  1:3829506/70‑1 (MQ=255)
                                       cATACAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtgg                            >  1:730411/1‑71 (MQ=255)
                                         tCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGt                                  <  1:2952952/63‑1 (MQ=255)
                                         tCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgt                              <  1:2602016/67‑1 (MQ=255)
                                         tCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAAAGCTGGt                                  <  1:3618731/63‑1 (MQ=255)
                                           cAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtggtg                          >  1:454512/1‑69 (MQ=255)
                                           cAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtggtg                          >  1:3942665/1‑69 (MQ=255)
                                            aGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTggtgggt                       <  1:3335724/71‑1 (MQ=255)
                                              ggCGCTGATGTGATTAATCGTCTGGGCGAATACCTg                                                        >  1:3172695/1‑36 (MQ=255)
                                              ggCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAg                               >  1:1229957/1‑61 (MQ=255)
                                                  cTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgt                              <  1:2199926/58‑1 (MQ=255)
                                                  cTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgt                              <  1:428980/58‑1 (MQ=255)
                                                    gATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAAtt               >  1:485440/1‑71 (MQ=255)
                                                    gATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAAt                >  1:247017/1‑70 (MQ=255)
                                                       gtgATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGa                                          <  1:3470388/41‑1 (MQ=255)
                                                       gtgATTAATCGGCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACa                   <  1:2573250/64‑1 (MQ=255)
                                                        tgATTAATCGTCTGGGCGAATACCTTAAGCCGCTGGCAGAACGCTGGTTAgtggt                           <  1:930896/55‑1 (MQ=255)
                                                        tgATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtggt                           <  1:2872112/55‑1 (MQ=255)
                                                        tgATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtggt                           <  1:2304898/55‑1 (MQ=255)
                                                        tgATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgtggt                           <  1:3703030/55‑1 (MQ=255)
                                                        tgATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGt            <  1:2185687/70‑1 (MQ=255)
                                                          aTTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGttt          >  1:46091/1‑70 (MQ=255)
                                                          aTTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGttt          >  1:1276756/1‑70 (MQ=255)
                                                          aTTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGttt          >  1:2961722/1‑70 (MQ=255)
                                                          aTTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGttt          >  1:2695180/1‑70 (MQ=255)
                                                          aTTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGttt          >  1:1394711/1‑70 (MQ=255)
                                                           ttAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgt                              <  1:951972/49‑1 (MQ=255)
                                                           ttAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGttt          >  1:2617900/1‑69 (MQ=255)
                                                             aaTCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAgt                              <  1:2465344/47‑1 (MQ=255)
                                                             aaTCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGTTTTAgg      >  1:3849954/1‑71 (MQ=255)
                                                              aTCGGCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGTTTTAgg      <  1:2158054/70‑1 (MQ=255)
                                                                cGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGTTTTAGGtt    >  1:3732285/1‑70 (MQ=255)
                                                                 gTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGtggtgg                         >  1:3726702/1‑48 (MQ=255)
                                                                 gTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGTTTTAGGtttt  >  1:1593958/1‑71 (MQ=255)
                                                                 gTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGTTTTAGGttt   <  1:1464225/70‑1 (MQ=255)
                                                                 gTCTGGGCGAATACCTGAAGCCGCTGCCAGAACGCTGGTTAGtggtgg                         >  1:3955883/1‑48 (MQ=255)
                                                                  |                                                                     
AGCAATTATGGACCGCATTATTCAATCACCGGGTAAATACATCCAGGGCGCTGATGTGATTAATCGTCTGGGCGAATACCTGAAGCCGCTGGCAGAACGCTGGTTAGTGGTGGGTGACAAATTTGTTTTAGGTTTT  >  W3110S.gb/3497639‑3497774

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