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	1,964,697	G→A	L118L (CTC→CTT)	flhA ←	putative flagellar export pore protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,964,697	0	G	A	100.0%	121.7 / NA	38	L118L (CTC→CTT)	flhA	putative flagellar export pore protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (20/18); total (20/18)

TACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTA  >  NC_000913/1964573‑1964811

tACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGaa                                                                                                      <  2:85010/139‑1 (MQ=255)

                  gcgcACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTccc                                                                                    >  1:913830/1‑139 (MQ=255)

                   cgcACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCt                                                                                   >  1:645943/1‑139 (MQ=255)

                             tCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGccgccgccg                                                                         <  2:478953/139‑1 (MQ=255)

                                    tACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGt                                                                  >  2:253434/1‑139 (MQ=255)

                                      cGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGTCGCCGCCGCGCCGTTAt                                                                >  2:525076/1‑139 (MQ=255)

                                                          gACCATAAAGTTGATGATCACG‑GAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATAc                                           >  1:134647/1‑139 (MQ=255)

                                                               tAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                            >  2:268207/1‑86 (MQ=255)

                                                               tAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGacc                                                                                            <  1:268207/86‑1 (MQ=255)

                                                               tAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGt                                       >  1:264827/1‑139 (MQ=255)

                                                                    ttGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAg                                  >  2:1203092/1‑139 (MQ=255)

                                                                      gatgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGATCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAACTGATAAGGGTGGAAGcc                                >  2:391479/1‑139 (MQ=255)

                                                                      gatgatCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGcc                                <  1:1116900/139‑1 (MQ=255)

                                                                            cACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTAt                                                                >  1:250548/1‑101 (MQ=255)

                                                                            cACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTAt                                                                <  2:250548/101‑1 (MQ=255)

                                                                            cACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTa                          >  2:1160060/1‑139 (MQ=255)

                                                                                      aCAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCcgccgccgc                                                                        >  1:1288631/1‑83 (MQ=255)

                                                                                      aCAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCcgccgccgc                                                                        <  2:1288631/83‑1 (MQ=255)

                                                                                       cAAACACCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACg               >  1:1252374/1‑139 (MQ=255)

                                                                                          acacCACGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCaa            >  2:1162522/1‑139 (MQ=255)

                                                                                            accacGATACCGCTAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTAAAGCCACGTTAAGTGCCAGACGCAACa          <  2:784903/139‑1 (MQ=255)

                                                                                            accacGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACa          <  1:1160060/139‑1 (MQ=255)

                                                                                               acGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGTCGCCGCCGCGCCGTTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCg       <  1:525076/139‑1 (MQ=255)

                                                                                                cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccc                                                            >  1:645227/1‑85 (MQ=255)

                                                                                                cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGccc                                                            <  2:645227/85‑1 (MQ=255)

                                                                                                cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGcc                    >  2:1291452/1‑125 (MQ=255)

                                                                                                cGATACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGcc                    <  1:1291452/125‑1 (MQ=255)

                                                                                                   tACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCcgccgccgc                                                                        >  2:330482/1‑70 (MQ=255)

                                                                                                   tACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCcgccgccgc                                                                        <  1:330482/70‑1 (MQ=255)

                                                                                                   tACCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGt   <  2:913830/139‑1 (MQ=255)

                                                                                                    aCCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTa  <  2:134647/139‑1 (MQ=255)

                                                                                                    aCCGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTa  <  1:1203092/139‑1 (MQ=255)

                                                                                                      cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCaa            >  1:502980/1‑127 (MQ=255)

                                                                                                      cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCaa            >  2:374283/1‑127 (MQ=255)

                                                                                                      cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCaa            <  1:374283/127‑1 (MQ=255)

                                                                                                      cGATAGCGAAATTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCaa            <  2:502980/127‑1 (MQ=255)

                                                                                                               aaTTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                      >  2:1214364/1‑76 (MQ=255)

                                                                                                               aaTTGCCACCAACAAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCAt                                                      <  1:1214364/76‑1 (MQ=255)

TACCATCGAGAACAAAGCGCGCACCCACTTCTGCGATACGCCCGGCACCTTTGGTAATGACCATAAAGTTGATGATCACGAGAATGACAAACACCACGATACCGATAGCGAAATTGCCACCAACGAGGAAGTGACCGAACGCTTCGACCACCTTCCCTGCCGCCGCCGCGCCGGTATGCCCTTCCATTAAAATGATACGGGTTGAAGCCACGTTAAGTGCCAGACGCAACAGCGTGGTA  >  NC_000913/1964573‑1964811

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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