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 2,863,108 T→C 13.2% L73L (TTA→CTA)  ygbM → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,863,1080TC13.2% 128.8 / 12.6 53L73L (TTA→CTA) ygbMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (20/26);  new base C (3/4);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.92e-01

GAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTGGAATATGCATTGG  >  W3110S.gb/2863039‑2863177
                                                                     |                                                                     
gAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGAt                                                                       >  1:3720210/1‑70 (MQ=255)
gAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGAt                                                                       >  1:4334056/1‑70 (MQ=255)
gAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGAt                                                                       >  1:4602708/1‑70 (MQ=255)
   cAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGAt                                                                       <  1:2615247/67‑1 (MQ=255)
     aaaCCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCg                                                                 >  1:525366/1‑71 (MQ=255)
             tGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGAt                                                                       >  1:898868/1‑57 (MQ=255)
             tGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTccc                                                         >  1:79603/1‑71 (MQ=255)
             tGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGACTATCCGCCCTTccc                                                         >  1:2489754/1‑71 (MQ=255)
                  cTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACg                                                    <  1:2645697/71‑1 (MQ=255)
                    ggCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGcc                                                               >  1:508512/1‑58 (MQ=255)
                     gcgcTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCgg                                                       >  1:1456660/1‑65 (MQ=255)
                     gcgcTGTTCAATAACGCTCCCGGAGATATTAATGCGGGGGAATGGGGACTATCCGCCCTTCCCGGACGt                                                   >  1:2141616/1‑69 (MQ=255)
                       gcTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGACTATCCGCCCTTCCCGGACGTGAGc                                               <  1:1474603/71‑1 (MQ=255)
                          gTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATcc                                                                  >  1:574321/1‑49 (MQ=255)
                          gTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTccc                                                         >  1:1332902/1‑58 (MQ=255)
                           ttCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCAc                                             <  1:3936181/69‑1 (MQ=255)
                           ttCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACg                                            <  1:4200199/70‑1 (MQ=255)
                             cAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTAt                                                                    >  1:2842914/1‑44 (MQ=255)
                             cAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGaa                                          <  1:1073119/70‑1 (MQ=255)
                              aaTACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAg                                         <  1:3052732/70‑1 (MQ=255)
                                tACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTc                                                           >  1:671103/1‑50 (MQ=255)
                                   cGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGca                                       <  1:2631205/67‑1 (MQ=255)
                                   cGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGca                                       <  1:3724524/67‑1 (MQ=255)
                                      tCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCa                                 <  1:397795/70‑1 (MQ=255)
                                        ccGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGAc                              <  1:2379464/71‑1 (MQ=255)
                                        ccGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTT‑‑CGGACGTGAGCACg                                            <  1:1598022/55‑1 (MQ=255)
                                          ggAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACAt                            <  1:4235408/71‑1 (MQ=255)
                                           gagaTATTAATGCGGGGGAATGGGGACTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATc                           <  1:344467/71‑1 (MQ=255)
                                           gagaTATTAATGCGGGGGAATGGGGACTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATc                           <  1:1683855/71‑1 (MQ=255)
                                            agaTATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATc                           >  1:2449771/1‑70 (MQ=255)
                                            agaTATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCg                          <  1:3915736/71‑1 (MQ=255)
                                             gaTATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGa                         <  1:662941/71‑1 (MQ=255)
                                               tatTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGaa                                          >  1:4127546/1‑52 (MQ=255)
                                                atTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCt                      >  1:3106308/1‑71 (MQ=255)
                                                 ttAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCa                                 <  1:2005664/59‑1 (MQ=255)
                                                 ttAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTg                     >  1:4193419/1‑71 (MQ=255)
                                                 ttAATGCGGGGGAATGGGGACTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCg                          <  1:2895901/66‑1 (MQ=255)
                                                   aaTGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGa                         >  1:1409262/1‑65 (MQ=255)
                                                   aaTGCGGGGGAATGGGGACTATCCGCCCTTCCCGGACGTGAGCACGAAGca                                       >  1:3445802/1‑51 (MQ=255)
                                                    aTGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGc                   <  1:1509555/70‑1 (MQ=255)
                                                    aTGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGc                   <  1:100954/70‑1 (MQ=255)
                                                    aTGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCa                  <  1:2392377/71‑1 (MQ=255)
                                                    aTGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCa                  <  1:4164582/71‑1 (MQ=255)
                                                      gCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACt                >  1:3027187/1‑71 (MQ=255)
                                                       cGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCa                  <  1:543946/68‑1 (MQ=255)
                                                         ggggAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTgg              <  1:558594/70‑1 (MQ=255)
                                                          gggAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTGGaa            <  1:4041143/71‑1 (MQ=255)
                                                           ggAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCa                                 <  1:2737609/49‑1 (MQ=255)
                                                              aTGGGGATTATCCTCCCTTCCCGGACGTGAGCACGAAGCACACGCa                                 <  1:4134870/46‑1 (MQ=255)
                                                               tGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGc                                        <  1:3358334/38‑1 (MQ=255)
                                                                ggggATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTGGAATATGc       <  1:1893420/70‑1 (MQ=255)
                                                                ggggATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTGGAATATGCa      >  1:1741096/1‑71 (MQ=255)
                                                                 gggATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGAc                        >  1:2550465/1‑52 (MQ=255)
                                                                 gggATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTGGAATATGCAt     >  1:846101/1‑71 (MQ=255)
                                                                  ggATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACa                             >  1:4270148/1‑46 (MQ=255)
                                                                  ggATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACAt                            >  1:420398/1‑47 (MQ=255)
                                                                   gATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTGGAATATGCATTg   <  1:2838344/71‑1 (MQ=255)
                                                                    aTTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTGGAATATGCATTgg  >  1:3259327/1‑71 (MQ=255)
                                                                     |                                                                     
GAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGTGAGCACGAAGCACACGCAGACATCGACCTGGCACTGGAATATGCATTGG  >  W3110S.gb/2863039‑2863177

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