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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,742,575 G→A intergenic (+14/+26) cfa → / ← ribC cyclopropane fatty acyl phospholipid synthase, SAM‑dependent/riboflavin synthase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,742,5750GA96.8% 191.0 / ‑0.7 62intergenic (+14/+26)cfa/ribCcyclopropane fatty acyl phospholipid synthase, SAM‑dependent/riboflavin synthase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (29/31);  minor base . (1/1);  total (30/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.79e-01

TTTAAACGAATGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCGCCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGATCGAT  >  NC_000913/1742439‑1742693
                                                                                                                                        |                                                                                                                       
tttAAACGAATGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCAcc                                                                                                                       <  2:866546/139‑1 (MQ=255)
  tAAACGAATGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCAcccc                                                                                                                     <  2:1217202/139‑1 (MQ=255)
  tAAACGAATGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCAcccc                                                                                                                     <  1:482039/139‑1 (MQ=255)
         aTGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCg                                                                                                              >  2:347138/1‑139 (MQ=255)
                      atCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAg                                                                                                 >  2:944848/1‑139 (MQ=255)
                           aaTGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTACAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAg                                                                                            <  1:944848/139‑1 (MQ=255)
                           aaTGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCgggg                                                                                                           <  1:1213425/124‑1 (MQ=255)
                           aaTGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCgggg                                                                                                           >  2:1213425/1‑124 (MQ=255)
                           aaTGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATC‑ACCCCTCTCCGGGGGc                                                                                                         >  2:420099/1‑125 (MQ=255)
                           aaTGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATC‑ACCCCTCTCCGGGGGc                                                                                                         <  1:420099/125‑1 (MQ=255)
                               ccTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCtt                                                                                        >  2:1148170/1‑139 (MQ=255)
                                  gtgCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGAtt                                                                                                     <  2:450053/123‑1 (MQ=255)
                                  gtgCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGAtt                                                                                                     >  1:450053/1‑123 (MQ=255)
                                   tgCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCtgt                                                                                    >  2:1511379/1‑139 (MQ=255)
                                             ttCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGa                                                                         >  2:880308/1‑139 (MQ=255)
                                                 gcgcCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGACGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCa                                                                     >  2:1316459/1‑139 (MQ=255)
                                                                  ctctGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGc                                                                                  <  2:432503/110‑1 (MQ=255)
                                                                  ctctGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGc                                                                                  >  1:432503/1‑110 (MQ=255)
                                                                  ctctGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgcc                                                    >  2:887133/1‑139 (MQ=255)
                                                                    ctGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgccgc                                                  <  1:1148170/139‑1 (MQ=255)
                                                                    ctGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgccgc                                                  >  1:1041653/1‑139 (MQ=255)
                                                                     tGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGc                                                                                                         >  2:779722/1‑84 (MQ=255)
                                                                     tGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGc                                                                                                         <  1:779722/84‑1 (MQ=255)
                                                                     tGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑gg                                                                             >  1:279750/1‑111 (MQ=255)
                                                                     tGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑gg                                                                             <  2:279750/111‑1 (MQ=255)
                                                                     tGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgccgcc                                                 <  1:347138/139‑1 (MQ=255)
                                                                     tGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCA‑TTTCTCGTGCCGCCa                                                >  1:202101/1‑139 (MQ=255)
                                                                       gCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGc                                                                                                         <  1:126724/82‑1 (MQ=255)
                                                                       gCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGc                                                                                                         >  2:126724/1‑82 (MQ=255)
                                                                        cAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGc                                              <  1:880308/139‑1 (MQ=255)
                                                                         aGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGca                                             <  1:887133/139‑1 (MQ=255)
                                                                          ggTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGCCTATTCTATCACCCCCTCTCCGGCGGCGATTTCAGATCACGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGcac                                            <  1:976908/139‑1 (MQ=255)
                                                                             cGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACg                                         <  2:1092636/139‑1 (MQ=255)
                                                                             cGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGACGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACg                                         <  1:1316459/139‑1 (MQ=255)
                                                                              gtgtTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACg                                         >  2:429247/1‑138 (MQ=255)
                                                                              gtgtTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACg                                         <  1:429247/138‑1 (MQ=255)
                                                                                 ttCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCTTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACg                                         >  1:1182469/1‑135 (MQ=255)
                                                                                 ttCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCTTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACg                                         <  2:1182469/135‑1 (MQ=255)
                                                                                  tctcACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTa                                    <  2:207330/139‑1 (MQ=255)
                                                                                      aCGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgccgcc                                                 >  1:1157778/1‑122 (MQ=255)
                                                                                      aCGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgccgcc                                                 <  2:1157778/122‑1 (MQ=255)
                                                                                         cgGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCg                                                                                                              >  2:1351310/1‑59 (MQ=255)
                                                                                         cgGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCg                                                                                                              <  1:1351310/59‑1 (MQ=255)
                                                                                           gtgtTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCTGGGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCt                            >  2:1091058/1‑139 (MQ=255)
                                                                                             gtTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGa                                                                                                <  2:646906/69‑1 (MQ=255)
                                                                                             gtTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGa                                                                                                >  1:646906/1‑69 (MQ=255)
                                                                                                      ggCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTg                                                                          >  1:384677/1‑81 (MQ=255)
                                                                                                      ggCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTg                                                                          <  2:384677/81‑1 (MQ=255)
                                                                                                      ggCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACg                                         >  1:1370230/1‑114 (MQ=255)
                                                                                                      ggCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACg                                         <  2:1370230/114‑1 (MQ=255)
                                                                                                      ggCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCCGGGGCGATTTCAGATCAGGCTACTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCGACCGTATCTACCACTGCCTGa                >  2:895821/1‑139 (MQ=255)
                                                                                                        ccTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgc                                                     >  1:872864/1‑100 (MQ=255)
                                                                                                        ccTTCGAGTGGCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgc                                                     <  2:872864/100‑1 (MQ=255)
                                                                                                                  gCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGc                                                                                                         >  1:326234/1‑39 (MQ=255)
                                                                                                                  gCTCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGc                                                                                                         <  2:326234/39‑1 (MQ=255)
                                                                                                                    tCGCTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGATCGAt  <  2:4968/139‑1 (MQ=255)
                                                                                                                       cTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgc                                                     >  1:254798/1‑85 (MQ=255)
                                                                                                                       cTAAAGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgc                                                     <  2:254798/85‑1 (MQ=255)
                                                                                                                         aaaGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGAt      >  1:1163862/1‑130 (MQ=255)
                                                                                                                         aaaGGCTATTCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGAt      <  2:1163862/130‑1 (MQ=255)
                                                                                                                                  tCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgcc                                                    <  1:382521/75‑1 (MQ=255)
                                                                                                                                  tCTATCACCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTgcc                                                    >  2:382521/1‑75 (MQ=255)
                                                                                                                                        |                                                                                                                       
TTTAAACGAATGTTTACCTATTATCTGAATGCCTGTGCAGGTGCTTTCCGCGCCCGTGATATTCAGCTCTGGCAGGTCGTGTTCTCACGCGGTGTTGAAAACGGCCTTCGAGTGGCTCGCTAAAGGCTATTCTATCGCCCCCTCTCCGGGGGCGATTTCAGATCAGGCTTCTGTGCCT‑GGTTGATTCATGGCATTTTCTCGTGCCGCCAGCACACGTTCTACCGTATCTACCACTGCCTGAGTTTGTGGATCGAT  >  NC_000913/1742439‑1742693

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A