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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 617,155 C→A 42.4% Q65K (CAA→AAA)  ycaL → predicted peptidase with chaperone function

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE617,1550CA42.4% 63.6 / 95.9 106Q65K (CAA→AAA) ycaLpredicted peptidase with chaperone function
Reads supporting (aligned to +/- strand):  ref base C (29/32);  new base A (20/25);  total (49/57)
Fisher's exact test for biased strand distribution p-value = 8.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 109 total aligned reads displayed.

AAGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACAA  >  minE/617094‑617222
                                                             |                                                                   
aaGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCACGTc                                                                >  1:2181198/1‑67 (MQ=255)
aaGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGt                                                                 >  1:20939/1‑66 (MQ=255)
aaGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTc                                                                >  1:1548175/1‑67 (MQ=255)
aaGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTc                                                                >  1:2850908/1‑67 (MQ=255)
aaGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTc                                                                >  1:3423876/1‑67 (MQ=255)
aaGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTc                                                                >  1:1412952/1‑67 (MQ=255)
aaGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTc                                                                >  1:2881211/1‑67 (MQ=255)
aaGCGATGCCGAAGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTc                                                                >  1:1348700/1‑67 (MQ=255)
     atgccgatgcAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGt                                                          >  1:1094688/1‑68 (MQ=255)
     atgccgatgcAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTa                                                         >  1:703561/1‑69 (MQ=255)
     atgccgatgcAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTa                                                         >  1:2416231/1‑69 (MQ=255)
     atgccgatgcAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTa                                                         >  1:621951/1‑69 (MQ=255)
     atgccgatgcAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTa                                                         >  1:355874/1‑69 (MQ=255)
     atgccgatgcAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTa                                                         >  1:837714/1‑69 (MQ=255)
     atgccgatgcAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTa                                                         >  1:842147/1‑69 (MQ=255)
     atgccgatgcAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTa                                                         >  1:3059249/1‑69 (MQ=255)
                aaaGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAg                                              <  1:1911010/69‑1 (MQ=255)
                       ttGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTa                                       <  1:2439693/69‑1 (MQ=255)
                       ttGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTa                                       <  1:1718614/69‑1 (MQ=255)
                       ttGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTa                                       <  1:2086742/69‑1 (MQ=255)
                               cAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCt                                >  1:2756439/1‑68 (MQ=255)
                               cAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCt                                >  1:926612/1‑68 (MQ=255)
                               cAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCt                                >  1:1598806/1‑68 (MQ=255)
                               cAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCt                                >  1:1546802/1‑68 (MQ=255)
                               cAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCt                                >  1:609569/1‑68 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:2959851/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:3014848/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:2808051/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:3425725/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:2736500/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:488109/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:689222/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:2354925/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:724470/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:2142873/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:877319/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:1014010/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:132166/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:1309342/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:190949/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:1157910/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:1778318/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:1288150/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:1366708/69‑1 (MQ=255)
                                  ggCTGTGTCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:1088220/69‑1 (MQ=255)
                                   gCTGTGTCCAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:2123430/68‑1 (MQ=255)
                                     tgtgCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCaaaa                         <  1:293428/69‑1 (MQ=255)
                                     tgtgCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCaaaa                         <  1:2827955/69‑1 (MQ=255)
                                     tgtgCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCaaaa                         <  1:3190178/69‑1 (MQ=255)
                                     tgtgCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCaaaa                         <  1:2074820/69‑1 (MQ=255)
                                      gtgtCGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:1628310/65‑1 (MQ=255)
                                       tgCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAATTACGGTAAACGTCTGGCaaaa                         >  1:2646844/1‑67 (MQ=255)
                                       tgCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAAt                       >  1:16725/1‑69 (MQ=255)
                                       tgCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAAt                       >  1:901180/1‑69 (MQ=255)
                                       tgCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAAt                       >  1:2606061/1‑69 (MQ=255)
                                         tcGATATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:891201/61‑1 (MQ=255)
                                         tcGAAATGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCa                            <  1:2095957/61‑1 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAATCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:252159/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACg                                          >  1:2275917/1‑44 (MQ=38)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTgg                              >  1:2272110/1‑56 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATc                      >  1:3112079/1‑64 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:2995445/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:354971/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:2108146/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:2182558/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:3131665/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:3078932/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:1346211/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:2226952/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:1082924/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:297827/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:2294459/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:2339939/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:2024753/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:2773926/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:1781174/1‑69 (MQ=255)
                                             aaTGGACAGCGGCAATAAAGTGGCAAGCAAATCCAGCAAGTACGGGAAACGTCTGGCAAAAATCGCCaa                 >  1:815124/1‑69 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCaaaa                         <  1:3391805/58‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:1193835/69‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:523912/69‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:1145775/69‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:1011112/69‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:1106539/69‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:3038985/69‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:302321/69‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:2045515/69‑1 (MQ=255)
                                                ggACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGc              <  1:2445483/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:2084587/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:1319462/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:2205516/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:1025832/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:2259864/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:2278056/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:2671760/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:1190221/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:1403169/69‑1 (MQ=255)
                                                            tCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  <  1:3352461/69‑1 (MQ=255)
                                                             cAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  >  1:1962751/1‑68 (MQ=255)
                                                             cAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  >  1:75086/1‑68 (MQ=255)
                                                             cAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACaa  >  1:1811227/1‑68 (MQ=255)
                                                             |                                                                   
AAGCGATGCCGATGCAAAAGCGATTGCCAATCAGGGCTGTGCCGAAATGGACAGCGGCAATCAAGTCGCAAGTAAATCCAGCAAGTACGGTAAACGTCTGGCAAAAATCGCCAAAGCATTGGGTAACAA  >  minE/617094‑617222

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A