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
A2 F1 I1 R1	81	28.9	1316934	95.8%	1261622	113.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,440,918	T→C	T38A (ACT→GCT)	rpoA ←	RNA polymerase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,440,918	0	T	C	100.0%	166.6 / NA	45	T38A (ACT→GCT)	rpoA	RNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (23/22); total (23/22)

AGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAG  >  NC_000913/3440782‑3441052

aGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCGCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCAt                                                                                                                                      >  1:422874/1‑139 (MQ=255)

                             gCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAgg                                                                                                         <  1:186551/139‑1 (MQ=255)

                                             tACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGgcgtgcg                                                                                         >  2:599673/1‑139 (MQ=255)

                                             tACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGgcgtgcg                                                                                         <  1:513074/139‑1 (MQ=255)

                                                       gtaCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGTCGTACGTCGAACTCAc                                                                               >  2:629651/1‑139 (MQ=255)

                                                       gtaCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCAc                                                                               >  1:519251/1‑139 (MQ=255)

                                                         acacCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACtt                                                                             >  1:155315/1‑139 (MQ=255)

                                                          cacCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCa                                                                                                                           >  2:94593/1‑92 (MQ=255)

                                                          cacCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCa                                                                                                                           <  1:94593/92‑1 (MQ=255)

                                                            ccATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          >  1:565387/1‑139 (MQ=255)

                                                            ccATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          >  1:508742/1‑139 (MQ=255)

                                                            ccATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          <  2:155315/139‑1 (MQ=255)

                                                            ccATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          >  1:371868/1‑139 (MQ=255)

                                                            ccATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          <  2:270870/139‑1 (MQ=255)

                                                            ccATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          <  2:509797/139‑1 (MQ=255)

                                                            ccATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          <  2:565387/139‑1 (MQ=255)

                                                             cATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          <  2:149681/138‑1 (MQ=255)

                                                             cATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          >  1:149681/1‑138 (MQ=255)

                                                               tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGc                                                                                                                             <  2:185925/85‑1 (MQ=255)

                                                               tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGc                                                                                                                             >  1:185925/1‑85 (MQ=255)

                                                               tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGTCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          <  2:519245/136‑1 (MQ=255)

                                                               tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGTCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          >  1:519245/1‑136 (MQ=255)

                                                                cAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGat                                                                      >  1:350217/1‑139 (MQ=255)

                                                                       aaCCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAAcc                                                               >  2:233805/1‑139 (MQ=255)

                                                                            cGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGgcg                                                          <  1:599673/139‑1 (MQ=255)

                                                                              gTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGcgcg                                                        >  2:347751/1‑139 (MQ=255)

                                                                                       cAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGaa                                               >  2:60146/1‑139 (MQ=255)

                                                                                        aaCCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGaaa                                              <  2:519251/139‑1 (MQ=255)

                                                                                             ggCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTg                                         <  1:60146/139‑1 (MQ=255)

                                                                                             ggCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTg                                         <  1:233805/139‑1 (MQ=255)

                                                                                                aTCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTca                                      <  2:508742/139‑1 (MQ=255)

                                                                                                    aTGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGa                                  >  1:409527/1‑139 (MQ=255)

                                                                                                              aaTACGGCGCAGTGCGTTACCCAGAGCATGGCCATAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCAtt                        <  2:422874/139‑1 (MQ=255)

                                                                                                              aaTACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCAtt                        >  1:539370/1‑139 (MQ=255)

                                                                                                                  cGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTgtgt                    <  2:371868/139‑1 (MQ=255)

                                                                                                                   ggCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTc                   <  2:225659/139‑1 (MQ=255)

                                                                                                                     cgcAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          >  1:461897/1‑82 (MQ=255)

                                                                                                                     cgcAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                          <  2:461897/82‑1 (MQ=255)

                                                                                                                     cgcAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGgcg                                                          <  1:100914/98‑1 (MQ=255)

                                                                                                                     cgcAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGgcg                                                          >  2:100914/1‑98 (MQ=255)

                                                                                                                     cgcAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTcaca                                    <  1:253681/120‑1 (MQ=255)

                                                                                                                     cgcAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTcaca                                    >  2:253681/1‑120 (MQ=255)

                                                                                                                       cAGTGCGTTCCCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCctct               <  1:220371/139‑1 (MQ=255)

                                                                                                                        aGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCctctc              >  2:281459/1‑139 (MQ=255)

                                                                                                                                    agagCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAg  >  2:112682/1‑139 (MQ=255)

AGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAG  >  NC_000913/3440782‑3441052

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