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
A12 F1 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,081,877	T→C	intergenic (‑242/‑36)	tktA ← / → loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,081,877	0	T	C	100.0%	216.4 / NA	59	intergenic (‑242/‑36)	tktA/loiP	transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (32/27); total (32/27)

TGGAACATCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTTTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGC  >  NC_000913/3081750‑3082007

tGGAACATCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATc                                                                                                                         >  2:50680/1‑139 (MQ=255)

     cATCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGAc                                                                                                                    >  1:1277401/1‑139 (MQ=255)

      aTCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGAcc                                                                                                                   >  2:562526/1‑139 (MQ=255)

      aTCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGAcc                                                                                                                   <  1:209342/139‑1 (MQ=255)

      aTCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGAcc                                                                                                                   >  2:465059/1‑139 (MQ=255)

        ccTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCtt                                                                                                                 >  1:413747/1‑139 (MQ=255)

           tttGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTtgtg                                                                                                              <  1:562526/139‑1 (MQ=255)

           tttGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTtgtg                                                                                                              <  2:415799/139‑1 (MQ=255)

                  cTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAaga                                                                                                       >  1:25135/1‑139 (MQ=255)

                                  aTCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTc                                                                                       >  2:137052/1‑139 (MQ=255)

                                    cATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     <  2:1277401/139‑1 (MQ=255)

                                    cATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     <  2:25135/139‑1 (MQ=255)

                                     aTGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgcg                                                                                    >  2:72409/1‑139 (MQ=255)

                                      tGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTtgtg                                                                                                              <  1:352196/112‑1 (MQ=255)

                                      tGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTtgtg                                                                                                              >  2:352196/1‑112 (MQ=255)

                                      tGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTc                                                                                       >  2:322235/1‑135 (MQ=255)

                                      tGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTc                                                                                       <  1:322235/135‑1 (MQ=255)

                                                               gCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCa                                                          <  1:245741/139‑1 (MQ=255)

                                                                cccGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCaa                                                         <  1:465059/139‑1 (MQ=255)

                                                                cccGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCaa                                                         <  2:413747/139‑1 (MQ=255)

                                                                  cGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     >  1:699016/1‑109 (MQ=255)

                                                                  cGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     <  2:699016/109‑1 (MQ=255)

                                                                  cGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTAt                                                                              >  2:1238017/1‑116 (MQ=255)

                                                                  cGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTAt                                                                              <  1:1238017/116‑1 (MQ=255)

                                                                   gTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACgg                                                      >  1:225708/1‑139 (MQ=255)

                                                                                 tCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGc                                        <  2:80218/139‑1 (MQ=255)

                                                                                        actgagactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAata                                 <  1:87305/139‑1 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGaat                                                                                                                             >  1:689037/1‑43 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGaat                                                                                                                             <  2:689037/43‑1 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGaa                                                                                                                              >  1:736486/1‑42 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGaa                                                                                                                              <  2:736486/42‑1 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCg                                                                                                            >  1:663408/1‑60 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCg                                                                                                            <  2:663408/60‑1 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCgcgc                                                                                   >  1:768891/1‑85 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCgcgc                                                                                   <  2:768891/85‑1 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCgcgc                                                                                   <  2:223244/85‑1 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCgcgc                                                                                   >  1:223244/1‑85 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTATCAATGAGCGTGGCaa                                                         <  2:877777/111‑1 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCaa                                                         >  1:877777/1‑111 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGc                                        >  1:692819/1‑128 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGc                                        <  2:692819/128‑1 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  2:1180292/1‑139 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  2:958591/1‑139 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  1:24304/1‑139 (MQ=255)

                                                                                            agactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  2:157086/1‑139 (MQ=255)

                                                                                             gactgagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGAc                            >  2:1002243/1‑139 (MQ=255)

                                                                                                 gagCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCa                        >  2:8851/1‑139 (MQ=255)

                                                                                                  agCGTCGATTCACCTGCAAACGGCGCATTCTTAGaa                                                                                                                              >  2:612994/1‑36 (MQ=255)

                                                                                                  agCGTCGATTCACCTGCAAACGGCGCATTCTTAGaa                                                                                                                              <  1:612994/36‑1 (MQ=255)

                                                                                                  agCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     >  1:247962/1‑77 (MQ=255)

                                                                                                  agCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcgc                                                                                     <  2:247962/77‑1 (MQ=255)

                                                                                                  agCGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGAGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCaa                       >  2:938060/1‑139 (MQ=255)

                                                                                                    cGTCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACg                     <  1:157086/139‑1 (MQ=255)

                                                                                                      tCGATTCACCTGCAAACGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGa                   <  1:137052/139‑1 (MQ=255)

                                                                                                                    aaCGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcg                                                                                      >  1:803333/1‑58 (MQ=255)

                                                                                                                    aaCGGCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTcg                                                                                      <  2:803333/58‑1 (MQ=255)

                                                                                                                       ggCGCATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGc  >  2:919601/1‑139 (MQ=255)

                                                                                                                         cgcATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             >  1:146876/1‑110 (MQ=255)

                                                                                                                         cgcATTCTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGa                             <  2:146876/110‑1 (MQ=255)

TGGAACATCCTTTTGCCGCTTCAGAAATCTCTGGATCATGCTCGCATGTTGCGCAATCTACTCGCCCGTCCGCTGCGCTTTTCCTTATACTGAGACTGAGCGTCGATTCACCTGCAAACGGCGCATTTTTAGAATAATCCTGACCTTGTGCGGAAGAGAAAACATGAAAATTCGCGCCTTATTGGTAGCAATGAGCGTGGCAACGGTACTGACTGGTTGCCAGAATATGGACTCCAACGGACTGCTCTCATCAGGAGC  >  NC_000913/3081750‑3082007

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