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
A28 F56 I1 R1 120 79.0 2973134 95.3% 2833396 126.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 3,723,447 T→C T87T (ACT→ACC)  U712_19195 → putative transporter ywcJ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,723,4470TC98.3% 216.9 / ‑3.1 58coding (261/771 nt)U712_19195putative transporter ywcJ
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (17/40);  minor base . (0/1);  total (17/41)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

AGCCGCAAGCAAAACAGGCAGTTATTTCTCTATGGCGGATTCTCCGTTTGCTTTTCCGGCAGCCGCTGTCACATTCGGGGCCGCTATTCTGCTGATTGCTTACGGAGGCGGAGATTTA‑TTTACTGGCAACACTTTTTATTTCACTTATACCGCGCTCCGAAAAAAAATTCGCTGGCGAGACACCCTGTACCTGTGGATGTCAAGCTATGCCGGCAATTTGATCGGCGCCATTCTATTTGCCATTCTGATCAGCGCGACAGGG  >  CP006881/3723315‑3723576
                                                                                                                                     |                                                                                                                                 
aGCCGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAt                                                                                                                             <  1:141214/139‑1 (MQ=255)
aGCCGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAt                                                                                                                             <  7:161162/139‑1 (MQ=255)
aGCCGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAt                                                                                                                             <  6:302774/139‑1 (MQ=255)
aGCCGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAt                                                                                                                             <  5:7500/139‑1 (MQ=255)
aGCCGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAt                                                                                                                             <  4:150784/139‑1 (MQ=255)
aGCCGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAt                                                                                                                             <  3:251705/139‑1 (MQ=255)
aGCCGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAt                                                                                                                             <  7:325329/139‑1 (MQ=255)
  ccGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAttt                                                                                                                           <  6:12450/139‑1 (MQ=255)
  ccGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAttt                                                                                                                           <  5:287708/139‑1 (MQ=255)
  ccGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTAttt                                                                                                                           <  5:244237/139‑1 (MQ=255)
  ccGCAAGCAAAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCGATTCTGAGTTATGATTACGGAGGCGGTGAATTATTTTACGGGC‑ACACCtttttttt                                                                                                                           >  6:229118/1‑139 (MQ=255)
    gcaagcaaAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCa                                                                                                                         >  2:33282/1‑139 (MQ=255)
     caagcaaAACAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGGCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCAc                                                                                                                        <  1:206831/139‑1 (MQ=255)
             aCAGGCAGCTATTTCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACcg                                                                                                                <  7:75612/139‑1 (MQ=255)
                        tttCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGgaa                                                                                                      <  4:320298/138‑1 (MQ=255)
                        tttCTTTATGGCTGATTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGgaa                                                                                                      <  5:58819/138‑1 (MQ=255)
                                      aTTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCg                                                                                       >  5:21287/1‑139 (MQ=255)
                                      aTTCTCCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCGTATGATTGCTTACGGAGGCCGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCATCTGGCg                                                                                       >  8:128513/1‑139 (MQ=255)
                                         ctcCGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  7:253893/139‑1 (MQ=255)
                                         ctcCGTTTGCCTTTCCGGCAGCCGCGGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  3:207375/139‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  2:696/136‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  1:33282/136‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  1:29444/136‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  3:93149/136‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  5:66239/136‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  1:27554/136‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  3:127941/136‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGaca                                                                                  <  6:273297/138‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACAC‑CTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGaca                                                                                  <  3:79005/137‑1 (MQ=255)
                                            cGTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGACGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  1:9041/136‑1 (MQ=255)
                                            cGTTTGCATTTCCGGCAGCCGCTGTCACTTTCGGGGCAGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCgcga                                                                                    <  8:119434/136‑1 (MQ=255)
                                             gTTTGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACAcc                                                                                <  4:83837/139‑1 (MQ=255)
                                                tGCCTTTCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCta                                                                             >  7:244403/1‑138 (MQ=255)
                                                 gcctttCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACAccata                                                                             <  3:127431/135‑4 (MQ=255)
                                                 gcctttCCGGCAGCCGCTGTCACTTTCGGGGCCGCTATTCTGATGATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCta                                                                             <  4:336772/135‑2 (MQ=255)
                                                                                           atgATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAAt                                          >  4:287134/2‑131 (MQ=255)
                                                                                           atgATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAAt                                          <  3:287134/130‑1 (MQ=255)
                                                                                           atgATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCa                                  <  1:118304/138‑1 (MQ=255)
                                                                                           atgATTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCa                                  >  7:174210/2‑139 (MQ=255)
                                                                                              aTTGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTc                               >  4:292769/1‑139 (MQ=255)
                                                                                               ttGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCt                              <  6:21287/139‑1 (MQ=255)
                                                                                                tGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTgg                                                                                         >  5:326509/1‑79 (MQ=255)
                                                                                                tGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTgg                                                                                         <  6:326509/79‑1 (MQ=255)
                                                                                                tGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTtgt                                                                      <  4:137531/98‑1 (MQ=255)
                                                                                                tGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTtgt                                                                      >  3:137531/1‑98 (MQ=255)
                                                                                                tGCTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCtg                             >  4:73781/1‑138 (MQ=255)
                                                                                                  cTTACGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGtt                           >  2:127352/1‑139 (MQ=255)
                                                                                                     aCGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTg                         <  3:292769/138‑1 (MQ=255)
                                                                                                     aCGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTg                         <  1:2620/138‑1 (MQ=255)
                                                                                                     aCGGAGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCGGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGtttt                         <  2:150190/138‑2 (MQ=255)
                                                                                                         aGGCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCAtc                    <  8:174210/139‑2 (MQ=255)
                                                                                                           gCGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACACTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCt                  >  8:20727/1‑139 (MQ=255)
                                                                                                            cGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGc                        >  2:214314/1‑132 (MQ=255)
                                                                                                            cGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGc                        <  1:214314/132‑1 (MQ=255)
                                                                                                            cGGAGATTTA‑TTTACCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCt                  >  6:366425/1‑138 (MQ=255)
                                                                                                                         taCCGGCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCTGATCAGCGCGAc      <  8:244403/138‑1 (MQ=255)
                                                                                                                            cggCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCTGATCAGCGCGACggga  >  7:205336/2‑138 (MQ=255)
                                                                                                                            cggCAACACCTTTTATTTCACCTATACCGCGCTCCGGAAAAAAATCAGCTGGCGCGACACCCTATACTTGTGGATGTCAAGCTATGCCGGCAATTTAATCGGCGCCATTCTGTTTGCCATCCTGATCAGCGCGACggga  >  8:30251/2‑138 (MQ=255)
                                                                                                                                     |                                                                                                                                 
AGCCGCAAGCAAAACAGGCAGTTATTTCTCTATGGCGGATTCTCCGTTTGCTTTTCCGGCAGCCGCTGTCACATTCGGGGCCGCTATTCTGCTGATTGCTTACGGAGGCGGAGATTTA‑TTTACTGGCAACACTTTTTATTTCACTTATACCGCGCTCCGAAAAAAAATTCGCTGGCGAGACACCCTGTACCTGTGGATGTCAAGCTATGCCGGCAATTTGATCGGCGCCATTCTATTTGCCATTCTGATCAGCGCGACAGGG  >  CP006881/3723315‑3723576

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ 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