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
A13 F1 I2 R1	762	35.5	1545288	95.5%	1475750	117.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,911,417	C→T	745 (TAG→TAA)	relA ←	(p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,911,417	0	C	T	100.0%	197.4 / NA	61	745 (TAG→TAA)	relA	(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (39/22); total (39/22)

GATCCGCACCGCCGGTGAATTTCCCCAACGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCCTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGTTTGGTGTCGCT  >  NC_000913/2911289‑2911551

gATCCGCACCGCCGGTGAATTTCCCCAACGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGt                                                                                                                              >  2:395448/1‑139 (MQ=255)

gATCCGCACCGCCGGTGAATTTCCCCAACGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGt                                                                                                                              >  1:425669/1‑139 (MQ=255)

                      ccccAACGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAAc                                                                                                        <  1:395448/139‑1 (MQ=255)

                           aCGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCg                                                                                                   <  2:558505/139‑1 (MQ=255)

                               tttACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCa                                                                                                <  2:307748/138‑1 (MQ=255)

                               tttACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCa                                                                                                >  1:307748/1‑138 (MQ=255)

                                                cATAACCGTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCa                                                                                                <  1:497267/121‑1 (MQ=255)

                                                cATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCACCCGACGCGCGTCGATAACATCCGGCa                                                                                                >  2:497267/1‑121 (MQ=255)

                                                   aaCCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCa                                                                           >  2:711953/1‑139 (MQ=255)

                                                     cccTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                         <  1:713401/139‑1 (MQ=255)

                                                     cccTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                         <  2:696681/139‑1 (MQ=255)

                                                          tCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCAAGTGCAACCGACGCGCGTCGATAACATCAGGCACCTGGTAGAGTTTACCCAGAACGCGccc                                                                    >  2:751154/1‑139 (MQ=255)

                                                               aaaCCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCa                                                               >  2:706600/1‑139 (MQ=255)

                                                                             tGTCGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTaa                                                 <  2:80350/139‑1 (MQ=255)

                                                                                  aTACAGTATATATCAATCTACATTGTAGTTACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAAtctc                                            >  1:608017/1‑139 (MQ=255)

                                                                                  aTACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAg                                                        >  1:494715/1‑127 (MQ=255)

                                                                                  aTACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAg                                                        <  2:494715/127‑1 (MQ=255)

                                                                                  aTACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAAtctc                                            >  2:138683/1‑139 (MQ=255)

                                                                                  aTACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAAtctc                                            >  1:498103/1‑139 (MQ=255)

                                                                                    aCAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAACACGCGCCCCAGCACTTGCAGGTTGTAAATCTCaa                                          >  2:669960/1‑139 (MQ=255)

                                                                                      aGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGt                                                                                                               >  2:726044/1‑68 (MQ=255)

                                                                                      aGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGt                                                                                                               >  1:235096/1‑68 (MQ=255)

                                                                                      aGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGt                                                                                                               <  1:726044/68‑1 (MQ=255)

                                                                                      aGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGt                                                                                                               <  2:235096/68‑1 (MQ=255)

                                                                                      aGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATg                                        >  2:538958/1‑139 (MQ=255)

                                                                                       gTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATgg                                       >  2:355581/1‑139 (MQ=255)

                                                                                       gTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATgg                                       >  2:718894/1‑139 (MQ=255)

                                                                                         atatatCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGAcgcg                                                                                                                  <  2:465685/62‑1 (MQ=255)

                                                                                         atatatCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGAcgcg                                                                                                                  >  1:465685/1‑62 (MQ=255)

                                                                                          tatatTAATCTACATTGTAGATACGAGCAAATTTCGCCTTAACTCCCGTGCAACCTACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCa                                    >  1:565511/1‑139 (MQ=255)

                                                                                            tatCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCa                                                                                                <  2:131209/77‑1 (MQ=255)

                                                                                            tatCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCa                                                                                                >  1:131209/1‑77 (MQ=255)

                                                                                             atCAATCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGt                                 >  2:431230/1‑139 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGc                                                                                                 <  2:176476/70‑1 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGc                                                                                                 >  1:176476/1‑70 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTgg                                                                                           >  2:733116/1‑76 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTgg                                                                                           <  1:733116/76‑1 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTATCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATg                            >  2:571302/1‑139 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                         <  1:111809/94‑1 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCAcg                                                                         >  2:111809/1‑94 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACgcgc                                                                      <  1:333672/97‑1 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACgcgc                                                                      >  2:333672/1‑97 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAg                                                                 <  1:695955/102‑1 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAg                                                                 >  2:695955/1‑102 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCa                                                         >  2:627486/1‑110 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCa                                                         <  1:627486/110‑1 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAg                                                        >  2:548175/1‑111 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAg                                                        <  1:548175/111‑1 (MQ=255)

                                                                                                  tCTACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATg                            >  1:398107/1‑139 (MQ=255)

                                                                                                    tACATTGTAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGt                          >  1:125808/1‑139 (MQ=255)

                                                                                                           tAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGt                   >  2:601839/1‑139 (MQ=255)

                                                                                                           tAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGt                   >  1:742959/1‑139 (MQ=255)

                                                                                                           tAGATACGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGt                   >  2:145232/1‑139 (MQ=255)

                                                                                                                aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGc                                                                                                 <  1:116964/56‑1 (MQ=255)

                                                                                                                aCGAGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGc                                                                                                 >  2:116964/1‑56 (MQ=255)

                                                                                                                   aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAgg                                                       >  1:90916/1‑95 (MQ=255)

                                                                                                                   aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAgg                                                       <  2:90916/95‑1 (MQ=255)

                                                                                                                   aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGttt           >  2:719493/1‑139 (MQ=255)

                                                                                                                   aGCAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGttt           >  1:326036/1‑139 (MQ=255)

                                                                                                                     cAAATTTCGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGTTTgg         >  2:659320/1‑139 (MQ=255)

                                                                                                                            cGGCTTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGTTTGGTGTCGCt  <  2:742959/139‑1 (MQ=255)

GATCCGCACCGCCGGTGAATTTCCCCAACGCTTTACGCTACTGTGGATCATAACCCTTTCCTCAAACCGCTATCATATGTAGATACAGTATATATCAATCTACATTGTAGATACGAGCAAATTTCGGCCTAACTCCCGTGCAACCGACGCGCGTCGATAACATCCGGCACCTGGTTGAGTTTACCCAGCACGCGCCCCAGCACTTGCAGGTTGTAAATCTCAATGGTCATGTCGATGGTCGCCAGTTGCTGTTTGGTGTCGCT  >  NC_000913/2911289‑2911551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `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