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 1,487,609 C→T 18.2% R926R (CGC→CGT)  hrpA → ATP‑dependent helicase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,487,6090CT18.2% 129.1 / 20.6 55R926R (CGC→CGT) hrpAATP‑dependent helicase
Reads supporting (aligned to +/- strand):  ref base C (27/18);  new base T (5/5);  total (32/23)
Fisher's exact test for biased strand distribution p-value = 7.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAACTATGCCGAAGCGTTTTTAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACC  >  W3110S.gb/1487540‑1487679
                                                                     |                                                                      
aaaCTATGCCGAAGCGTTTTTAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGcgcg                                                                       <  1:1724403/71‑1 (MQ=255)
 aaCTATGCCGAAGCGTTTTTAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGa                                                                      <  1:4095863/71‑1 (MQ=255)
   cTATGCCGAAGCGTTTTTAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGTGAGt                                                                    >  1:4109184/1‑71 (MQ=255)
   cTATGCCGAAGCGTTTTTAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGTGAGt                                                                    >  1:691034/1‑71 (MQ=255)
          gAAGCGTTTTTAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTAcggcg                                                             <  1:867143/71‑1 (MQ=255)
                tttttAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGcgcg                                                                       <  1:4481079/55‑1 (MQ=255)
                tttttAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGAc                                                       >  1:3397746/1‑71 (MQ=255)
                 ttttAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGAcc                                                      >  1:2825930/1‑71 (MQ=255)
                  tttAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGAc                                                       >  1:1547810/1‑69 (MQ=255)
                  tttAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCg                                                     >  1:1607832/1‑71 (MQ=255)
                         cgcgTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTAc                                              >  1:1660699/1‑71 (MQ=255)
                            gTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGt                                           >  1:2591727/1‑71 (MQ=255)
                             tCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGtt                                                                   <  1:2714142/46‑1 (MQ=255)
                             tCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGAc                                                       <  1:2690386/58‑1 (MQ=255)
                             tCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGtt                                          <  1:853219/71‑1 (MQ=255)
                               aaaCCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAg                                                                     >  1:3713331/1‑42 (MQ=255)
                               aaaCCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAg                                                                     >  1:3389756/1‑42 (MQ=255)
                               aaaCCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAg                                                                     >  1:1205921/1‑42 (MQ=255)
                               aaaCCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAg                                                                     >  1:1590736/1‑42 (MQ=255)
                               aaaCCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTAc                                                                 >  1:4037274/1‑46 (MQ=255)
                                 aCCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGAcc                                      >  1:2367108/1‑71 (MQ=255)
                                  ccGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAg                                                                     >  1:940604/1‑39 (MQ=255)
                                   cGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGt                                                                    <  1:748117/39‑1 (MQ=255)
                                   cGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGt                                                                    <  1:922156/39‑1 (MQ=255)
                                   cGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGt                                                                    <  1:604973/39‑1 (MQ=255)
                                   cGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACcgc                                    >  1:2767956/1‑71 (MQ=255)
                                   cGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACcgc                                    >  1:909796/1‑71 (MQ=255)
                                    gCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTAcg                                                                <  1:2006433/42‑1 (MQ=255)
                                     cTGGAGTTACCGTTGCTCGACAGCCTTGAGCGTGAGTTACGGCGGATGACCGGCGTTACCGTTGACcgcg                                   >  1:4235338/1‑70 (MQ=255)
                                     cTGGAGTTACCGTTGCTCGACAGCCTTGAGCGTGAGTTACGGCGGATGACCGGCGTTACCGTTGACcgcg                                   >  1:1475610/1‑70 (MQ=255)
                                     cTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTAc                                              <  1:3207558/59‑1 (MQ=255)
                                        gAGTTACCGTTGCTCGACAGCCTTGAGCGTGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGaa                                 <  1:1669291/69‑1 (MQ=255)
                                        gAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGa                               <  1:2688524/71‑1 (MQ=255)
                                           ttACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGaa                                 >  1:3190481/1‑66 (MQ=255)
                                           ttACCGTTGCTCGACAGCCTTGAGAGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGaa                                 >  1:1056916/1‑66 (MQ=255)
                                            tACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAg                                <  1:83395/66‑1 (MQ=255)
                                             aCCGTTGCTCGACAGCCTTGAGCGTGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTgg                           >  1:2695506/1‑70 (MQ=255)
                                              ccGTTGCTCGACAGCCTT‑AGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCAc                        <  1:2770018/71‑1 (MQ=255)
                                               cGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCAc                        <  1:4339366/71‑1 (MQ=255)
                                               cGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGAACGCGAAGACTGGCAc                        <  1:1852781/71‑1 (MQ=255)
                                                gTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACt                       <  1:998492/71‑1 (MQ=255)
                                                  tGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGa                               >  1:464978/1‑61 (MQ=255)
                                                   gCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTg                                         >  1:2997340/1‑50 (MQ=255)
                                                   gCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTgg                     >  1:3484841/1‑70 (MQ=255)
                                                    cTCGACAGCCTTGAGCGTGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTggg                    <  1:2902095/70‑1 (MQ=255)
                                                     tCGACAGCCTTGAGCGCGAGATACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGAt                  >  1:3335103/1‑71 (MQ=255)
                                                      cGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGAt                  >  1:2333660/1‑70 (MQ=255)
                                                      cGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATc                 >  1:619338/1‑71 (MQ=255)
                                                      cGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATc                 >  1:3720396/1‑71 (MQ=255)
                                                       gACAGCCTTGAGCGTGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATc                 <  1:468041/70‑1 (MQ=255)
                                                       gACAGCCTTGAGCGTGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCa                <  1:2696987/71‑1 (MQ=255)
                                                       gACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGAt                  <  1:3548589/69‑1 (MQ=255)
                                                         cAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCa                >  1:4434588/1‑69 (MQ=255)
                                                               tGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGccc         >  1:2732523/1‑70 (MQ=255)
                                                                taGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCg        <  1:4385826/69‑1 (MQ=255)
                                                                gAGCGTGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCg        <  1:739839/70‑1 (MQ=255)
                                                                gAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCACGa       >  1:1128586/1‑71 (MQ=255)
                                                                    gcgAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGa                               >  1:3038793/1‑43 (MQ=255)
                                                                     cgAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCAcc  <  1:4644908/71‑1 (MQ=255)
                                                                     cgAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCAcc  <  1:3876571/71‑1 (MQ=255)
                                                                     cgAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCAcc  >  1:232812/1‑71 (MQ=255)
                                                                     cgAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATAAGGTGCCCGATCAcc  >  1:1750863/1‑71 (MQ=255)
                                                                     |                                                                      
AAACTATGCCGAAGCGTTTTTAGGCCGCGTCAAACCGCTGGAGTTACCGTTGCTCGACAGCCTTGAGCGCGAGTTACGGCGGATGACCGGCGTTACCGTTGACCGCGAAGACTGGCACTGGGATCAGGTGCCCGATCACC  >  W3110S.gb/1487540‑1487679

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