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 1,263,012 T→A 40.2% I57I (ATA→ATT)  cutC ← copper homeostasis protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,263,0120TA40.2% 50.1 / 92.7 97I57I (ATA→ATT) cutCcopper homeostasis protein
Reads supporting (aligned to +/- strand):  ref base T (21/37);  new base A (27/12);  total (48/49)
Fisher's exact test for biased strand distribution p-value = 1.88e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.56e-01

Only 100 of 106 total aligned reads displayed.

CCTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGCC  >  minE/1262951‑1263080
                                                             |                                                                    
ccTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGC‑AAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:2358533/69‑1 (MQ=255)
 cTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:3107011/69‑1 (MQ=255)
 cTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:746065/69‑1 (MQ=255)
 cTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:3297298/69‑1 (MQ=255)
 cTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:2528118/69‑1 (MQ=255)
 cTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:1120823/69‑1 (MQ=255)
 cTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:3043824/69‑1 (MQ=255)
 cTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:2826755/69‑1 (MQ=255)
   cAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              >  1:1661394/1‑67 (MQ=255)
   cAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              >  1:3196843/1‑67 (MQ=255)
        aTGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAggg                                                       >  1:264642/1‑69 (MQ=255)
        aTGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAggg                                                       >  1:2397994/1‑69 (MQ=255)
        aTGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAggg                                                       >  1:2130393/1‑69 (MQ=255)
        aTGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAggg                                                       >  1:486537/1‑69 (MQ=255)
        aTGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAggg                                                       >  1:3063282/1‑69 (MQ=255)
           gcggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATc                                                    >  1:146948/1‑69 (MQ=255)
           gcggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATc                                                    >  1:1884725/1‑69 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:2473248/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:3348459/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:3270037/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:1195172/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:1675369/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:2388614/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:1565699/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:3206347/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:1555962/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:3120631/69‑1 (MQ=255)
             ggcAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:1428726/69‑1 (MQ=255)
              acAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGGATAATCGGATGCACTGGGATCGt                                                  <  1:3266171/67‑1 (MQ=255)
               cAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATg                                                              <  1:3269009/55‑1 (MQ=255)
                   cTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCg                                            >  1:2659133/1‑69 (MQ=255)
                   cTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCg                                            >  1:428486/1‑69 (MQ=255)
                   cTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCg                                            >  1:316262/1‑69 (MQ=255)
                   cTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCg                                            >  1:201631/1‑69 (MQ=255)
                   cTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCg                                            >  1:3261893/1‑69 (MQ=255)
                     cACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGt                                                  >  1:857997/1‑61 (MQ=255)
                     cACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGc                                           >  1:3093077/1‑68 (MQ=255)
                     cACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCt                                          <  1:2468957/69‑1 (MQ=255)
                     cACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCt                                          >  1:1231177/1‑69 (MQ=255)
                     cACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCt                                          >  1:2616729/1‑69 (MQ=255)
                     cACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCt                                          >  1:3428501/1‑69 (MQ=255)
                     cACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCt                                          >  1:1715144/1‑69 (MQ=255)
                              tGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACg                                  <  1:3079299/68‑1 (MQ=255)
                              tGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACg                                  <  1:2632542/68‑1 (MQ=255)
                              tGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACg                                  <  1:2684187/68‑1 (MQ=255)
                              tGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACg                                  <  1:334498/68‑1 (MQ=255)
                              tGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACg                                  <  1:2767168/68‑1 (MQ=255)
                              tGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACg                                  <  1:1316378/68‑1 (MQ=255)
                               gTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACg                                  <  1:2318884/67‑1 (MQ=255)
                               gTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACg                                  <  1:1985351/67‑1 (MQ=255)
                                     aaaaTCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGTATTTCAg                          <  1:617351/69‑1 (MQ=255)
                                     aaaaTCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAg                          <  1:2045688/69‑1 (MQ=255)
                                     aaaaTCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAg                          <  1:1918423/69‑1 (MQ=255)
                                     aaaaTCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAg                          <  1:1742397/69‑1 (MQ=255)
                                     aaaaTCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAg                          <  1:609495/69‑1 (MQ=255)
                                     aaaaTCACCACCGCCTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAg                          <  1:1098094/69‑1 (MQ=255)
                                             caccGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACAccc                   <  1:1099401/68‑1 (MQ=255)
                                             caccGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACAccc                   <  1:2549490/68‑1 (MQ=255)
                                             caccGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACAccc                   <  1:1705933/68‑1 (MQ=255)
                                             caccGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACAccc                   <  1:950027/68‑1 (MQ=255)
                                             caccGCGTGGGCGAATTATCGGATGCACAGGGATCGACACCCGCTGGCGCACGGATTTCAGTACAccc                   <  1:1135016/68‑1 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:71049/1‑69 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:300793/1‑69 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:700336/1‑69 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:2299263/1‑69 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:2827386/1‑69 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:1557285/1‑69 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:182610/1‑69 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:3377573/1‑69 (MQ=255)
                                                 gcgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACCCCCAacga              >  1:2535260/1‑69 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCCGTac                       >  1:2123630/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:359758/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:3256305/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:1024513/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:2966206/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:101692/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:1131182/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:1447723/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:1523692/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:153691/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:1538839/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:189637/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:2138905/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:2740363/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:3107792/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:2931817/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTac                       >  1:2517021/1‑59 (MQ=255)
                                                  cgTGGGCGGATAATCGGATGCACTGGGATCGTCACCCGCTGGCGCACGGATTTCAGTa                        >  1:1092417/1‑58 (MQ=255)
                                                      ggCGAATTATCGGATGCACAGGGATCGTCACCCGCt                                          <  1:1901463/36‑1 (MQ=255)
                                                          aaTTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTaa     <  1:2277666/69‑1 (MQ=255)
                                                          aaTTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTaa     <  1:1155394/69‑1 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACAGCCAACGACGGCGTTAAGcc  >  1:1062677/1‑69 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGcc  >  1:24756/1‑69 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGcc  >  1:1912656/1‑69 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGcc  >  1:269150/1‑69 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGcc  >  1:605310/1‑69 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGcc  >  1:2810209/1‑69 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGcc  >  1:1447325/1‑69 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGcc  >  1:206023/1‑69 (MQ=255)
                                                             tATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGcc  >  1:241381/1‑69 (MQ=255)
                                                             |                                                                    
CCTCAAGAATGGCGGCAAACTCACCGTCGCTGTAGCAAAAATCACCACCGCGTGGGCGAATTATCGGATGCACAGGGATCGTCACCCGCTGGCGCACGGATTTCAGTACACCCAACGACGGCGTTAAGCC  >  minE/1262951‑1263080

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