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 F1 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,897,050 +G coding (277/666 nt) yieH → phosphoenolpyruvate and 6‑phosphogluconate phosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,897,0461.G97.4% 129.7 / ‑3.3 38coding (273/666 nt)yieHphosphoenolpyruvate and 6‑phosphogluconate phosphatase
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (18/19);  total (19/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

TTTCAAAGGTGTAAAACTGTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑A‑GGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATGCAGCATTCTATGGGCAAGCTGAATATGTTGCACTACTTCCCGGATAAACTGTTCAGCGGC  >  NC_000913/3896908‑3897178
                                                                                                                                            |                                                                                                                                    
tttCAAAGGTGTAAAACTGTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGa‑a                                                                                                                                       >  1:480205/1‑139 (MQ=255)
tttCAAAGGTGTAAAACTGTACGAAATTATCGATATTGTGTCCCTTGAACATGGCGTTACGTTAGCGAAAACAGAAGCTGAACATGTTTACCGTGCAGAAGTCGCTCGGCTGTTCTATTCAGAACTGGAAGCCATCGa‑a                                                                                                                                       >  2:747695/1‑139 (MQ=255)
  tCAAAGGTGTAAAACTGTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑A‑gg                                                                                                                                    >  2:358331/1‑139 (MQ=255)
           tAAAACTGTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAg                                                                                                                            >  1:182241/1‑139 (MQ=255)
           tAAAACTGTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAg                                                                                                                            >  1:448370/1‑139 (MQ=255)
                  gTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGa‑a                                                                                                                                       >  1:139776/1‑121 (MQ=255)
                  gTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGa‑a                                                                                                                                       <  2:139776/121‑1 (MQ=255)
                  gTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCt                                                                                                                     >  2:5777/1‑139 (MQ=255)
                  gTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCt                                                                                                                     >  1:796778/1‑139 (MQ=255)
                  gTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCt                                                                                                                     >  1:66676/1‑139 (MQ=255)
                  gTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑A‑ggg                                                                                                                                   >  1:1085351/1‑124 (MQ=255)
                  gTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑A‑ggg                                                                                                                                   <  2:1085351/124‑1 (MQ=255)
                   tACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTg                                                                                                                    >  2:724413/1‑139 (MQ=255)
                   tACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTg                                                                                                                    <  1:358331/139‑1 (MQ=255)
                   tACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTg                                                                                                                    >  1:827951/1‑139 (MQ=255)
                         aTTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCg                                                                                                              <  2:827951/139‑1 (MQ=255)
                                  atTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTgcg                                                                                                     <  2:796778/139‑1 (MQ=255)
                                    tGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAgcg                                                                                                                          >  1:1019891/1‑116 (MQ=255)
                                    tGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAgcg                                                                                                                          <  2:1019891/116‑1 (MQ=255)
                                     gTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCa                                                                                                  <  2:333857/139‑1 (MQ=255)
                                     gTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCa                                                                                                  <  1:5777/139‑1 (MQ=255)
                                       ttCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAAt                                                                                                <  2:480205/139‑1 (MQ=255)
                                       ttCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAAt                                                                                                <  1:323784/139‑1 (MQ=255)
                                         cccTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGa‑a                                                                                                                                       <  2:551139/98‑1 (MQ=255)
                                         cccTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGa‑a                                                                                                                                       >  1:551139/1‑98 (MQ=255)
                                           cTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAAtgtgt                                                                                            >  1:524209/1‑139 (MQ=255)
                                            ttGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAAtgtgtg                                                                                           <  2:524209/139‑1 (MQ=255)
                                             tGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAAtgtgtgt                                                                                          >  1:903143/1‑139 (MQ=255)
                                              gAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAAtgtgtg                                                                                           >  1:27175/1‑137 (MQ=255)
                                              gAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAAtgtgtg                                                                                           <  2:27175/137‑1 (MQ=255)
                                                        ttACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACg                                                                               >  1:591988/1‑139 (MQ=255)
                                                              tAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGAGG‑GGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCaa                                                                         >  2:812727/1‑139 (MQ=255)
                                                                gCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGa‑a                                                                                                                                       <  2:639415/75‑1 (MQ=255)
                                                                gCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGa‑a                                                                                                                                       >  1:639415/1‑75 (MQ=255)
                                                                     aaCAGAAGCTGAACACGTTTACCGTGCAGAAGTCGGTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACaa                                                                  >  2:113882/1‑139 (MQ=255)
                                                                     aaCAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCa                                                                                                  >  2:509111/1‑107 (MQ=255)
                                                                     aaCAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCa                                                                                                  <  1:509111/107‑1 (MQ=255)
                                                                      aCAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACaaa                                                                 <  1:812727/139‑1 (MQ=255)
                                                                            gCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATgcag                                                           <  1:1035621/139‑1 (MQ=255)
                                                                                       ttACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATGCAGCATTCTATggg                                                <  1:67798/139‑1 (MQ=255)
                                                                                             tGCAGAAGTCGCTCGGCTGTGCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATGCAGCATTCTATGGGCaa                                             >  2:666381/1‑136 (MQ=255)
                                                                                             tGCAGAAGTCGCTCGGCTCTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATGCAGCATTCTATGGGCaa                                             <  1:666381/136‑1 (MQ=255)
                                                                                                    gTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATaa                                                                     <  1:403542/105‑1 (MQ=255)
                                                                                                    gTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATaa                                                                     >  2:403542/1‑105 (MQ=255)
                                                                                                       gCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGTCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATgcag                                                           <  1:313761/112‑1 (MQ=255)
                                                                                                       gCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGTCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATgcag                                                           >  2:313761/1‑112 (MQ=255)
                                                                                                                  cGATTCAGAACTGGAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATGCAGCATTCTATGGGCAAGCTGAATATGTTGCACTACTTccc                     <  1:113882/139‑1 (MQ=255)
                                                                                                                               gAAGCCATCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATGCAGCATTCTATGGGCAAGCTGAATATGTTGCACTACTTCCCGGATAAACTGTTc        >  2:518937/1‑139 (MQ=255)
                                                                                                                                     aTCGA‑AGGGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATGCAGCATTCTATGGGCAAGCTGAATATGTTGCACTACTTCCCGGATAAACTGTTCAGCGGc  <  2:591988/139‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                    
TTTCAAAGGTGTAAAACTGTACGAAATTATCGATATTGTTTCCCTTGAACATGGTGTTACGTTAGCGAAAACAGAAGCTGAACACGTTTACCGTGCAGAAGTCGCTCGGCTGTTCGATTCAGAACTGGAAGCCATCGA‑A‑GGGGCTGGAGCGCTCCTGTCAGCGATCACTGCGCCAATGTGTGTGGTATCTAACGGCCCAAATAACAAAATGCAGCATTCTATGGGCAAGCTGAATATGTTGCACTACTTCCCGGATAAACTGTTCAGCGGC  >  NC_000913/3896908‑3897178

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A