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
A14 F1 I1 R1	770	68.5	3470224	91.7%	3182195	103.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,967,135	G→A	R434C (CGT→TGT)	ptsP ←	PEP‑protein phosphotransferase enzyme I, GAF domain containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,967,135	0	G	A	93.8%	181.4 / 1.8	64	R434C (CGT→TGT)	ptsP	PEP‑protein phosphotransferase enzyme I, GAF domain containing protein
Reads supporting (aligned to +/- strand): ref base G (2/2); new base A (30/30); total (32/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

CCTGTTCTTCTTCCGACGGGAAACCACTTTGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACGCTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTACCGGCTCCGGATCGACCAGCAATTCAC  >  NC_000913/2966997‑2967263

ccTGTTCTTCTTCCGACGGGAAACCACTTTGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACg                                                                                                                                  >  1:294638/1‑139 (MQ=255)

     tcttcttcCGACGGGAAACCACTTTGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCAc                                                                                                                             <  2:417772/139‑1 (MQ=255)

     tcttcttcCGACGGGAAACCACTTTGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCAc                                                                                                                             <  1:71123/139‑1 (MQ=255)

              gACGGGAAACCACTTTGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCttttaa                                                                                                                    >  1:576098/1‑137 (MQ=255)

               aCGGGAAACCACTTTGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTaa                                                                                                                   >  2:141307/1‑139 (MQ=255)

               aCGGGAAACCACTTTGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTaa                                                                                                                   >  2:128908/1‑139 (MQ=255)

                             tGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAAt                                                                                                     >  2:1338897/1‑139 (MQ=255)

                                   aTGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGt                                                                                               <  2:734440/139‑1 (MQ=255)

                                    tGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTc                                                                                              >  2:342460/1‑139 (MQ=255)

                                          ggATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTc                                                                                        >  2:102129/1‑139 (MQ=255)

                                            aTTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCg                                                                                      >  2:476958/1‑139 (MQ=255)

                                            aTTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCg                                                                                      <  1:1338897/139‑1 (MQ=255)

                                              ttCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCAc                                                                                                                             <  1:1444913/98‑1 (MQ=255)

                                              ttCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCAc                                                                                                                             >  2:1444913/1‑98 (MQ=255)

                                              ttCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGcc                                                                                    >  2:886739/1‑139 (MQ=255)

                                                 aGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACGCTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGa                                                                                 <  2:294638/139‑1 (MQ=255)

                                                      gATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCt                                                                            <  2:1673168/139‑1 (MQ=255)

                                                          aaGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGc                                                                        <  1:102129/139‑1 (MQ=255)

                                                               cGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCaa                                                                    >  2:776224/1‑138 (MQ=255)

                                                               cGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCaa                                                                    <  1:776224/138‑1 (MQ=255)

                                                                gATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAAtc                                                                  >  1:63868/1‑139 (MQ=255)

                                                                 aTGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCt                                                                            >  2:1604226/1‑128 (MQ=255)

                                                                 aTGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCt                                                                            <  1:1604226/128‑1 (MQ=255)

                                                                 aTGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAAtct                                                                 >  1:444849/1‑139 (MQ=255)

                                                                 aTGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAAtct                                                                 >  1:1143770/1‑139 (MQ=255)

                                                                 aTGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAAtct                                                                 <  1:342460/139‑1 (MQ=255)

                                                                     cATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTc                                                             <  2:1143770/139‑1 (MQ=255)

                                                                              ggCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAg                                                    <  1:476958/139‑1 (MQ=255)

                                                                               gCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACGCTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGc                                                   >  1:834889/1‑139 (MQ=255)

                                                                                ttccgcattttttCATCGTGTTCCCGGCTTGAGCCACCATTGAGCATGAGATGTATGCGCTCACCGCGTTTTAACTGCGCGTGTAAATTTACGTCATCTTCCTGCAGACGGCTAAGCTCAATCTCTGCGCGAATTAGcc                                                  <  2:834889/131‑1 (MQ=255)

                                                                                 tGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGc                                                   <  2:1654671/137‑1 (MQ=255)

                                                                                 tGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGc                                                   >  1:1654671/1‑137 (MQ=255)

                                                                                   cccAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCAc                                                                                                                             <  1:1690743/61‑1 (MQ=255)

                                                                                   cccAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCAc                                                                                                                             >  2:1690743/1‑61 (MQ=255)

                                                                                   cccAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGc                                                                             >  1:648197/1‑109 (MQ=255)

                                                                                   cccAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGc                                                                             <  2:648197/109‑1 (MQ=255)

                                                                                   cccAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAAt                                                                   >  1:560526/1‑119 (MQ=255)

                                                                                   cccAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAAt                                                                   <  2:560526/119‑1 (MQ=255)

                                                                                                  tGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACt                                                                                                                                <  1:1156484/43‑1 (MQ=255)

                                                                                                  tGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACt                                                                                                                                >  2:1721346/1‑43 (MQ=255)

                                                                                                  tGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACACt                                                                                                                                >  2:1156484/1‑43 (MQ=255)

                                                                                                      ccGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTAc                            <  2:444849/139‑1 (MQ=255)

                                                                                                      ccGGGCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTAc                            <  2:63868/139‑1 (MQ=255)

                                                                                                        gggCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAAtt                                                      >  1:392739/1‑111 (MQ=255)

                                                                                                        gggCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAAtt                                                      <  2:392739/111‑1 (MQ=255)

                                                                                                        gggCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGc                                                   <  2:1593679/114‑1 (MQ=255)

                                                                                                        gggCTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGc                                                   >  1:1593679/1‑114 (MQ=255)

                                                                                                           cTTAAACCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTACCGGCt                       <  1:128908/139‑1 (MQ=255)

                                                                                                               aaCCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGc                                                                        <  1:841480/86‑1 (MQ=255)

                                                                                                               aaCCAGCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGc                                                                        >  2:841480/1‑86 (MQ=255)

                                                                                                                    gCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAAt                                                                   >  2:566662/1‑86 (MQ=255)

                                                                                                                    gCATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAAt                                                                   <  1:566662/86‑1 (MQ=255)

                                                                                                                    gCATTGAGCATGACTTTTATACACTCACCGC‑TTTTAACTGCGCGGTTAAATTGACGTCATCTTCCGCCAGACGTCTAAGCTCAATCTCGTCACAAATTAGCCGCTGATATTCTTGCAGCAGTACCGGCTCCGGATCGAc             <  2:576098/139‑1 (MQ=255)

                                                                                                                     cATTGAGCATGACTTTTATACGCTCACCGCTTTTTAACTgcg                                                                                                              >  1:1036626/1‑42 (MQ=255)

                                                                                                                     cATTGAGCATGACTTTTATACGCTCACCGCTTTTTAACTgcg                                                                                                              <  2:1036626/42‑1 (MQ=255)

                                                                                                                     cATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTg                                                                                                                <  2:167109/40‑1 (MQ=255)

                                                                                                                     cATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTg                                                                                                                >  1:167109/1‑40 (MQ=255)

                                                                                                                     cATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTg                                     <  2:1651458/115‑1 (MQ=255)

                                                                                                                     cATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTg                                     >  1:1651458/1‑115 (MQ=255)

                                                                                                                     cATTGAGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTACCGGCTCCGGATCGAc             >  1:1093959/1‑139 (MQ=255)

                                                                                                                          aGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCtt                                                              <  2:1689908/85‑1 (MQ=255)

                                                                                                                          aGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCtt                                                              >  1:1689908/1‑85 (MQ=255)

                                                                                                                          aGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTAc                            >  2:933412/1‑119 (MQ=255)

                                                                                                                          aGCATGACTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCACCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTAc                            <  1:933412/119‑1 (MQ=255)

                                                                                                                                aCTTTTATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTACCGGCTCCGGATCGACCAGCAATTCAc  <  1:886739/139‑1 (MQ=255)

                                                                                                                                    ttATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTAc                            <  2:1101477/109‑1 (MQ=255)

                                                                                                                                    ttATACACTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTAc                            >  1:1101477/1‑109 (MQ=255)

CCTGTTCTTCTTCCGACGGGAAACCACTTTGCAGCATGAATGGGATTTCAGTGCGATAAAGACCGATGCCATCAATACGGCTGCCCAGTTTTTCTTCATGTTCCGGGCTTAAACCAGCATTGAGCATGACTTTTATACGCTCACCGCTTTTTAACTGCGCGGGTAAATTGACGTCATCTTCCGCCAGACGGCTAAGCTCAATCTCTTCACTAATTAGCCGCTGATATTCTTGCAGCAGTACCGGCTCCGGATCGACCAGCAATTCAC  >  NC_000913/2966997‑2967263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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