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	92	50.6	2362856	94.3%	2228173	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	685,425	T→C	T169A (ACC→GCC)	gltK ←	glutamate/aspartate ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	685,425	0	T	C	100.0%	126.6 / NA	35	T169A (ACC→GCC)	gltK	glutamate/aspartate ABC transporter permease
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/16); total (19/16)

ACGCGCTAAGACTAATAACGAAATAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGTATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGCGCGGCGCTCGATTGACCACG  >  NC_000913/685293‑685557

acgCGCTAAGACTAATAACGAAATAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTg                                                                                                                                >  1:191778/1‑139 (MQ=255)

          aCTAATAACGAAATAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACg                                                                                                                      <  1:19000/139‑1 (MQ=255)

              ataaCGAAATAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGc                                                                                                                  >  1:762865/1‑139 (MQ=255)

                aaCGAAATAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGccc                                                                                                                >  1:970013/1‑139 (MQ=255)

                    aaaTAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACg                                                                                                                      <  2:218016/129‑1 (MQ=255)

                    aaaTAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACg                                                                                                                      >  1:218016/1‑129 (MQ=255)

                    aaaTAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCtgag                                                                                                            >  2:1166978/1‑139 (MQ=255)

                                      aaCAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCa                                                                                          <  1:1166978/139‑1 (MQ=255)

                                           gATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATcgcg                                                                                     <  2:191778/139‑1 (MQ=255)

                                                   cAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGc                                                                             >  2:650874/1‑139 (MQ=255)

                                                          cGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGc                                                                      >  2:1114497/1‑139 (MQ=255)

                                                          cGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGc                                                                      <  1:650874/139‑1 (MQ=255)

                                                                   aCGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATc                                                             >  1:744216/1‑139 (MQ=255)

                                                                    cGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCa                                                            <  1:1114497/139‑1 (MQ=255)

                                                                       tCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGagca                                                                                                      >  1:1076722/1‑94 (MQ=255)

                                                                       tCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGagca                                                                                                      <  2:1076722/94‑1 (MQ=255)

                                                                           cAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCAt                                                     >  2:119591/1‑139 (MQ=255)

                                                                                      gCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGt                                          >  1:766389/1‑139 (MQ=255)

                                                                                      gCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGt                                          <  2:970013/139‑1 (MQ=255)

                                                                                          tACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTAc                                                                                                                       <  1:203878/58‑1 (MQ=255)

                                                                                          tACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTAc                                                                                                                       >  2:203878/1‑58 (MQ=255)

                                                                                          tACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGt                                      >  1:115265/1‑139 (MQ=255)

                                                                                                    aTCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGaataat                                                              <  1:684737/105‑1 (MQ=255)

                                                                                                    aTCGGCCAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGaataat                                                              >  2:684737/1‑105 (MQ=255)

                                                                                                         ccAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAg                       <  1:119591/139‑1 (MQ=255)

                                                                                                         ccAGGGATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAg                       >  2:1008075/1‑139 (MQ=255)

                                                                                                             ggATAACACATACACCAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGcgcg                   <  2:766389/139‑1 (MQ=255)

                                                                                                                           ccAGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGCGCGGCGCTCGATTGAcc     <  1:1008075/139‑1 (MQ=255)

                                                                                                                             aGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGCGCGGCGCTCGATTGACCAc   >  2:1062027/1‑139 (MQ=255)

                                                                                                                             aGTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGCGCGGCGCTCGATTGACCAc   <  2:744216/139‑1 (MQ=255)

                                                                                                                              gTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGcgcg                   >  2:182528/1‑122 (MQ=255)

                                                                                                                              gTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGcgcg                   <  1:182528/122‑1 (MQ=255)

                                                                                                                              gTGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGCGCGGCGCTCGATTGACCACg  >  2:376790/1‑139 (MQ=255)

                                                                                                                               tGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGCGCGGCGCTCGATTGAc      >  2:131667/1‑134 (MQ=255)

                                                                                                                               tGAGGCATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGCGCGGCGCTCGATTGAc      <  1:131667/134‑1 (MQ=255)

ACGCGCTAAGACTAATAACGAAATAAACAAATCCGGCAAACAGGATCATCTCAACCTGCGTACCATCACGCTCACCAATGGTTGAGGCGGTACGGAAGAAATCGGCCAGGGATAACACATACACCAGTGAGGTATCCTGGAACAGTACGATGCCCTGAGTGAGCAGCAGCGGCACCATCGCGCGGAACGCCTGCGGCAGAATAATCAGTTTCATCGACTGCCAGTGAGTCATTCCCAACGCCAGCGCGGCGCTCGATTGACCACG  >  NC_000913/685293‑685557

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A