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
A9 F1 I2 R1	760	52.7	2744488	90.2%	2475528	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	969,352	G→A	329 (TAG→TAA)	lpxK →	lipid A 4'kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	969,352	0	G	A	100.0%	121.0 / NA	38	329 (TAG→TAA)	lpxK	lipid A 4'kinase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (17/21); total (17/21)

GCGGTGAAATGCCGGGCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGCACAAGGCCTGTTAAACAAACCCCGCCGTCGAGCGT  >  NC_000913/969230‑969476

gCGGTGAAATGCCGGGCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCgg                                                                                                                   <  1:750333/134‑1 (MQ=255)

gCGGTGAAATGCCGGGCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCgg                                                                                                                   >  2:750333/1‑134 (MQ=255)

gCGGTGAAATGCCGGGCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCg                                                                                                              >  2:1339044/1‑139 (MQ=255)

    tGAAATGCCGGGCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCg                                                                                                          <  1:671675/139‑1 (MQ=255)

            cGGGCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATgg                                                                                                  >  1:358552/1‑139 (MQ=255)

             gggCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGa                                                                                                 <  1:142331/139‑1 (MQ=255)

             gggCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGa                                                                                                 >  2:542741/1‑139 (MQ=255)

                    tGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCgg                                                                                                                   >  2:933237/1‑114 (MQ=255)

                    tGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCgg                                                                                                                   <  1:933237/114‑1 (MQ=255)

                                          ttGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTccc                                                                    <  2:1260151/139‑1 (MQ=255)

                                                 tAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGa                                                             >  2:504439/1‑139 (MQ=255)

                                                       cacaGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCgg                                                                                                                   <  1:274874/79‑1 (MQ=255)

                                                       cacaGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCgg                                                                                                                   >  2:274874/1‑79 (MQ=255)

                                                       cacaGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGcgcg                                                       <  1:504439/139‑1 (MQ=255)

                                                       cacaGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGcgcg                                                       <  1:1339044/139‑1 (MQ=255)

                                                           gCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACct                                                                         >  1:1196944/1‑117 (MQ=255)

                                                           gCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACct                                                                         <  2:1196944/117‑1 (MQ=255)

                                                               tCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTc                                               >  2:1141750/1‑139 (MQ=255)

                                                                     gatgaACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTg                                         <  1:1141750/139‑1 (MQ=255)

                                                                      atgaACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTa                                                                                                                           <  1:1064492/56‑1 (MQ=255)

                                                                      atgaACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTa                                                                                                                           >  2:1064492/1‑56 (MQ=255)

                                                                      atgaACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCAc                                                                           <  2:646794/104‑1 (MQ=255)

                                                                      atgaACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCAc                                                                           >  1:646794/1‑104 (MQ=255)

                                                                        gaACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCa                                                                                                                 <  1:268864/64‑1 (MQ=255)

                                                                        gaACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCa                                                                                                                 >  2:268864/1‑64 (MQ=255)

                                                                         aaCCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGc                                     >  1:942183/1‑139 (MQ=255)

                                                                              gCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGCACAAg                                <  2:942183/139‑1 (MQ=255)

                                                                                gAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGCACAAGGc                              <  2:1057916/139‑1 (MQ=255)

                                                                                      gCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGAt                                                                                                        >  1:925268/1‑59 (MQ=255)

                                                                                      gCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGAt                                                                                                        <  2:925268/59‑1 (MQ=255)

                                                                                       cTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGCACAAGGCCTGTTaa                       <  1:542741/139‑1 (MQ=255)

                                                                                       cTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGACAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCg                                                                              >  2:1271851/1‑84 (MQ=255)

                                                                                       cTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGACAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCg                                                                              <  1:1271851/84‑1 (MQ=255)

                                                                                                cTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGcc                                                                               <  1:976663/74‑1 (MQ=255)

                                                                                                cTAACCTTGCTGGCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGcc                                                                               >  2:976663/1‑74 (MQ=255)

                                                                                                            gCTTCTGGCAACTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGCACAAGGCCTGTTAAACAAACCCCGCCGTCGAGcgt  <  2:1212529/139‑1 (MQ=255)

                                                                                                                      aCTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGcac                                   >  2:280765/1‑96 (MQ=255)

                                                                                                                      aCTAATTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGcac                                   <  1:280765/96‑1 (MQ=255)

GCGGTGAAATGCCGGGCCTTTGCAGAAGAAAATTGGTGGTATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGCACCTCTCCCTTGCTGATGCGCGTAATCTTCACCTTGCCGCACAAGGCCTGTTAAACAAACCCCGCCGTCGAGCGT  >  NC_000913/969230‑969476

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A