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
A10 F1 I2 R1	757	38.1	1607544	96.5%	1551279	117.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,440,950	G→A	T27I (ACC→ATC)	rpoA ←	RNA polymerase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,440,950	0	G	A	100.0%	106.9 / NA	35	T27I (ACC→ATC)	rpoA	RNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (19/16); total (19/16)

TACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGGAGTAAAGCTCGACGATCAGGTGT  >  NC_000913/3440827‑3441085

tACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGgcgtgcg                                                                                                                          <  1:344831/139‑1 (MQ=255)

          gtaCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCAc                                                                                                                >  2:66299/1‑139 (MQ=255)

          gtaCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCAc                                                                                                                <  1:636276/139‑1 (MQ=255)

                cATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTc                                                                                                          >  2:79975/1‑139 (MQ=255)

                cATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTc                                                                                                          >  2:399174/1‑139 (MQ=255)

                  tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTACAGGCTCACGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGa                                                                                                        >  1:344974/1‑139 (MQ=255)

                  tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGa                                                                                                        >  2:729441/1‑139 (MQ=255)

                  tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGa                                                                                                        >  2:333115/1‑139 (MQ=255)

                   cAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGaa                                                                                                                     <  2:557674/125‑1 (MQ=255)

                   cAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGaa                                                                                                                     >  1:557674/1‑125 (MQ=255)

                     aTCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                                                           <  1:224086/133‑1 (MQ=255)

                     aTCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                                                           >  2:224086/1‑133 (MQ=255)

                     aTCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGatat                                                                                                     >  2:164642/1‑139 (MQ=255)

                     aTCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGatat                                                                                                     >  1:210649/1‑139 (MQ=255)

                                 gTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGcgcg                                                                                         >  1:304177/1‑139 (MQ=255)

                                 gTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGcgcg                                                                                         >  2:176708/1‑139 (MQ=255)

                                              ccGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAActc                                                                            <  1:66299/139‑1 (MQ=255)

                                                     cGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTcaca                                                                     <  2:304177/139‑1 (MQ=255)

                                                     cGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTcaca                                                                     <  1:729441/139‑1 (MQ=255)

                                                       aTGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGa                                                                   <  1:399174/139‑1 (MQ=255)

                                                                gAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCAt                                                          >  2:288503/1‑139 (MQ=255)

                                                                 aaTACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCAtt                                                         <  1:164642/139‑1 (MQ=255)

                                                                      ggCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTc                                                    <  2:210649/139‑1 (MQ=255)

                                                                      ggCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTc                                                    >  2:55965/1‑139 (MQ=255)

                                                                        cgcAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGgcgtgcg                                                                                                                          >  1:602302/1‑67 (MQ=255)

                                                                        cgcAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGgcgtgcg                                                                                                                          <  2:602302/67‑1 (MQ=255)

                                                                        cgcAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCct                                                  <  1:288503/139‑1 (MQ=255)

                                                                                                   aaGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGgcgc                                                                                          >  1:556861/1‑72 (MQ=255)

                                                                                                   aaGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGgcgc                                                                                          <  2:556861/72‑1 (MQ=255)

                                                                                                   aaGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCct                                                  <  2:289352/112‑1 (MQ=255)

                                                                                                   aaGCCACGCTCTAAAGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCct                                                  >  1:289352/1‑112 (MQ=255)

                                                                                                                aaGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCt                                                              >  2:344764/1‑87 (MQ=255)

                                                                                                                aaGGCTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCt                                                              <  1:344764/87‑1 (MQ=255)

                                                                                                                    cTCAAGGATCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGGAGTAAAGCTCGACGATCAg      <  1:754881/139‑1 (MQ=255)

                                                                                                                        aGGATCACCTTGGCGTGCGTCGAACTCACTTACTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGGAGTAAAGCTCGACGATCAGgtgt  >  2:214833/1‑139 (MQ=255)

TACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGGAGTAAAGCTCGACGATCAGGTGT  >  NC_000913/3440827‑3441085

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