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 I2 R1	94	59.5	3027142	91.9%	2781943	108.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,426,492	A→G	R99R (CGT→CGC)	hisJ ←	histidine ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,426,492	0	A	G	100.0%	146.6 / NA	40	R99R (CGT→CGC)	hisJ	histidine ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (19/21); total (19/21)

GGGTGGTGCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGACGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATAATTCCTTTGCCAG  >  NC_000913/2426359‑2426626

gggTGGTGCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGttt                                                                                                                                   <  2:466487/139‑1 (MQ=255)

      tgCCCTGCAATACGCCTTCCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGt                                                                                                                             >  2:757896/1‑139 (MQ=255)

              actACGCCTACCCGTTTGCTTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGGCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGaaa                                                                                                                     <  2:390128/137‑1 (MQ=255)

                     cTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGa                                                                                                              >  2:1370939/1‑139 (MQ=255)

                                   ttCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCaa                                                                                                <  1:1482087/139‑1 (MQ=255)

                                    tCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAAt                                                                                               >  1:1421897/1‑139 (MQ=255)

                                          actcgactGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATcttctt                                                                                         <  1:846381/139‑1 (MQ=255)

                                          actcgactGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATcttctt                                                                                         >  2:846381/1‑139 (MQ=255)

                                                    cGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                                       >  2:646240/1‑99 (MQ=255)

                                                    cGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                                       <  1:646240/99‑1 (MQ=255)

                                                        tGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACg                                                                           >  1:1567/1‑139 (MQ=255)

                                                          aaTGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACggg                                                                         >  1:196862/1‑139 (MQ=255)

                                                                                 ccaAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTc                                                  <  2:1567/139‑1 (MQ=255)

                                                                                   aaaCGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGa                                                <  2:402489/139‑1 (MQ=255)

                                                                                   aaaCGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGa                                                <  1:757896/139‑1 (MQ=255)

                                                                                   aaaCGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGa                                                <  1:177916/139‑1 (MQ=255)

                                                                                     aCGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTCCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACa                                              <  1:799655/139‑1 (MQ=255)

                                                                                         gaATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGa                                                >  1:347651/1‑133 (MQ=255)

                                                                                         gaATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGa                                                <  2:347651/133‑1 (MQ=255)

                                                                                          aaTCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGa                                                <  1:63304/132‑1 (MQ=255)

                                                                                          aaTCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGa                                                >  2:63304/1‑132 (MQ=255)

                                                                                          aaTCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGt                                         <  1:566796/139‑1 (MQ=255)

                                                                                          aaTCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGt                                         >  2:347685/1‑139 (MQ=255)

                                                                                           aTCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                                       >  2:613878/1‑60 (MQ=255)

                                                                                           aTCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                                       <  1:613878/60‑1 (MQ=255)

                                                                                                 aGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGc                                  >  1:874660/1‑139 (MQ=255)

                                                                                                   cGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATcttctt                                                                                         <  2:221575/82‑1 (MQ=255)

                                                                                                   cGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATcttctt                                                                                         >  1:221575/1‑82 (MQ=255)

                                                                                                   cGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGAc                                                                            >  2:1210172/1‑95 (MQ=255)

                                                                                                   cGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGAc                                                                            <  1:1210172/95‑1 (MQ=255)

                                                                                                     tACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                                       >  2:1174367/1‑50 (MQ=255)

                                                                                                     tACAGTTTGTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGa                                                                                                                       <  1:1174367/50‑1 (MQ=255)

                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGt                      >  2:247446/1‑139 (MQ=255)

                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGt                      <  2:196862/139‑1 (MQ=255)

                                                                                                             gTCGGTGAAGGCTATTTCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGt                      <  2:874660/139‑1 (MQ=255)

                                                                                                                            ttCTTGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATAATTCCttt       >  1:662185/1‑139 (MQ=255)

                                                                                                                                tGCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATAATTCCTTTGCCa   <  1:247446/139‑1 (MQ=255)

                                                                                                                                 gCTGGCGTTTTTCCGTAATGGAAAGCGATGACatg                                                                                                          <  2:566517/35‑1 (MQ=255)

                                                                                                                                 gCTGGCGTTTTTCCGTAATGGAAAGCGATGACatg                                                                                                          >  1:566517/1‑35 (MQ=255)

                                                                                                                                 gCTGGCGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATAATTCCTTTGCCAg  >  2:1257586/1‑139 (MQ=255)

GGGTGGTGCCCTGCAATACGCCTACCCGTTTGCCTTTCAGCGACTCGACTGTCGGCTGAATGTCAGAATTTTTCGCCACCACCAAACGAGAATCGGCAGCGTACAGTTTGTCGGTGAAGGCTATTTCTTGCTGACGTTTTTCCGTAATGGAAAGCGATGACATGATGGCGTCAATCTTCTTCGCTTTTAAGGACGGGATTAACGCATCCAGCGGATTTTCGACAAACGTACATTGCGTATTGATGCGTTTGCATAATTCCTTTGCCAG  >  NC_000913/2426359‑2426626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `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