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
A11 F1 I2 R1	59	52.6	2411032	94.1%	2268781	113.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,535,392	C→T	P159P (CCG→CCA)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,535,392	0	C	T	100.0%	127.8 / NA	39	P159P (CCG→CCA)	envZ	sensory histidine kinase in two‑component regulatory system with OmpR
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (24/15); total (24/15)

CCTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGC  >  NC_000913/3535283‑3535527

ccTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGt                                                                                                            >  1:345991/1‑139 (MQ=255)

    cAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGc                                                                                                        <  1:798503/139‑1 (MQ=255)

      aGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCgg                                                                                                      <  2:434813/139‑1 (MQ=255)

      aGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCgg                                                                                                      <  1:72950/139‑1 (MQ=255)

          tGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCtgat                                                                                                                      <  2:661629/119‑1 (MQ=255)

          tGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCtgat                                                                                                                      >  1:661629/1‑119 (MQ=255)

            cGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAACCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcgcg                                                                                                >  1:1065226/1‑139 (MQ=255)

                ttCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTAcc                                                                                            <  2:773550/139‑1 (MQ=255)

                               cggtcggtTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATA‑TGGGCGACa                                                                            >  1:442829/1‑139 (MQ=255)

                                    ggtTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCa                                                                        >  2:348884/1‑139 (MQ=255)

                                                gAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCa                                                            >  2:407414/1‑139 (MQ=255)

                                                  aTAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAga                                                          >  2:849238/1‑139 (MQ=255)

                                                        aGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATA‑TGGGCGACAGCCAGGTTTTCAGCCAGACGACAgg                                                   <  2:442829/139‑1 (MQ=255)

                                                         gCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAgg                                                   <  1:849238/139‑1 (MQ=255)

                                                          ccACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGc                                                  >  1:135192/1‑139 (MQ=255)

                                                                        tCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTTGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGAc                                    >  2:635336/1‑139 (MQ=255)

                                                                                  cATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCgg                                                                                                      >  2:495697/1‑63 (MQ=255)

                                                                                  cATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCgg                                                                                                      <  1:495697/63‑1 (MQ=255)

                                                                                  cATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcg                                                                                                  <  2:842637/67‑1 (MQ=255)

                                                                                  cATAATCGCCAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcg                                                                                                  >  1:842637/1‑67 (MQ=255)

                                                                                          ccAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcgcg                                                                                                >  1:243428/1‑61 (MQ=255)

                                                                                          ccAGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCAcgcg                                                                                                <  2:243428/61‑1 (MQ=255)

                                                                                            aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGc                                                                          >  2:564289/1‑81 (MQ=255)

                                                                                            aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGc                                                                          <  1:564289/81‑1 (MQ=255)

                                                                                            aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGtttt                                                                  >  1:527287/1‑89 (MQ=255)

                                                                                            aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGtttt                                                                  <  2:527287/89‑1 (MQ=255)

                                                                                            aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAAcg                             >  1:515849/1‑126 (MQ=255)

                                                                                            aGCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAAcg                             <  2:515849/126‑1 (MQ=255)

                                                                                             gCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCgg               >  1:52729/1‑139 (MQ=255)

                                                                                             gCGTATAGCGGAACAGTGGAGAGAAATCGCCCTGATGAATTACGGTCAGGGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGCCAGGCGAACTTTTGTTAACCTCAACGCGCACTTCCGTCgg               >  2:1016167/1‑139 (MQ=255)

                                                                                                     cGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGa                                     >  1:1202231/1‑109 (MQ=255)

                                                                                                     cGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGa                                     <  2:1202231/109‑1 (MQ=255)

                                                                                                     cGGAACAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCa       >  1:477486/1‑139 (MQ=255)

                                                                                                        aaCAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGtt    >  1:31999/1‑139 (MQ=255)

                                                                                                        aaCAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGtt    >  2:911308/1‑139 (MQ=255)

                                                                                                         aCAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTTGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTtg   >  2:584753/1‑139 (MQ=255)

                                                                                                         aCAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTtg   <  1:407414/139‑1 (MQ=255)

                                                                                                          cAGTGGAGAGAAATCGCCCTGATGAATTTCTGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTtgc  >  1:719209/1‑139 (MQ=255)

                                                                                                          cAGTGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCg                   >  2:5969/1‑122 (MQ=255)

CCTGCAAGGCTGCGTGTTCGAGATCGACCAACGGTCGGTTCTGGATACGAATAAACAGCCACGCCCCGCCTATCGCCAATAGCATAATCGCCAGCGTATAGCGGAACAGCGGAGAGAAATCGCCCTGATGAATTTCGGTCAGCGGCACGCGTACCCAGATATTGGGCGACAGCCAGGTTTTCAGCCAGACGACAGGCGAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGC  >  NC_000913/3535283‑3535527

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A