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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,484,897	(C)_6→7	coding (524/3594 nt)	evgS →	hybrid sensory histidine kinase in two‑component regulatory system with EvgA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,484,891	1	.	C	100.0%	127.7 / NA	38	Y173S (TAC→TCC)	evgS	hybrid sensory histidine kinase in two‑component regulatory system with EvgA
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (17/21); total (17/21)

TTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACA  >  NC_000913/2484754‑2485013

ttCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑c                                                                                                                           >  1:611267/1‑139 (MQ=255)

  cgccgcCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑ccc                                                                                                                         >  2:532394/1‑139 (MQ=255)

   gccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑cccc                                                                                                                        >  1:440861/1‑139 (MQ=255)

    ccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑ccccc                                                                                                                       <  2:468542/139‑1 (MQ=255)

         tctTAATAATGACATTGCAGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑cccccccaga                                                                                                                  <  1:625331/139‑5 (MQ=255)

               taatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGt                                                                                                             <  2:894030/139‑1 (MQ=255)

                       ttGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATtcatc                                                                                                     >  1:181108/1‑139 (MQ=255)

                       ttGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATtcatc                                                                                                     >  1:624158/1‑139 (MQ=255)

                          ctgcAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCCACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGATGTTATTCatcaat                                                                                                  >  2:207012/1‑139 (MQ=255)

                                         tGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaa                                                                                   <  2:832942/139‑1 (MQ=255)

                                                tACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTAt                                                                            <  2:181108/139‑1 (MQ=255)

                                                      tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaaca                                                                                 >  1:322571/1‑128 (MQ=255)

                                                      tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaaca                                                                                 <  2:322571/128‑1 (MQ=255)

                                                        cGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                    <  1:337145/139‑1 (MQ=255)

                                                            gcTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACaaa                                                                >  1:502317/1‑139 (MQ=255)

                                                             cTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAAt                                                               <  2:502317/139‑1 (MQ=255)

                                                                  aaCCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTtata                                                          <  2:849901/139‑1 (MQ=255)

                                                                        ccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATc                                                        <  1:361804/135‑1 (MQ=255)

                                                                        ccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATc                                                        >  2:361804/1‑135 (MQ=255)

                                                                          ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                    >  2:789902/1‑121 (MQ=255)

                                                                          ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                    <  1:789902/121‑1 (MQ=255)

                                                                          ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCAt                                                  <  2:845412/139‑1 (MQ=255)

                                                                          ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCAt                                                  >  1:845412/1‑139 (MQ=255)

                                                                            cACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTa                                                >  2:17878/1‑139 (MQ=255)

                                                                            cACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTa                                                >  1:229088/1‑139 (MQ=255)

                                                                               gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                             <  2:229088/139‑1 (MQ=255)

                                                                                aCTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCCCGGGTAGCAAATTACCCCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                             <  1:380970/139‑1 (MQ=255)

                                                                                      tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTACCCCCCCCAGAGGAGTTAATTCATAATTCATTTCCAAAAGCACAAATTATCTCTTTTAAAAATTTATATAAGCCATTAGCATCCGtc                                       >  2:380970/1‑139 (MQ=255)

                                                                                      tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACTAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                      <  2:611267/139‑1 (MQ=255)

                                                                                      tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                      >  2:837248/1‑139 (MQ=255)

                                                                                           ccGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCt                                 <  1:17878/139‑1 (MQ=255)

                                                                                           ccGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCt                                 >  2:456905/1‑139 (MQ=255)

                                                                                           ccGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑ccccccca                                                                                                                    <  1:282350/55‑3 (MQ=255)

                                                                                           ccGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑ccccccca                                                                                                                    >  2:282350/1‑53 (MQ=255)

                                                                                              cTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                      <  1:625119/131‑1 (MQ=255)

                                                                                              cTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTggg                              >  2:35274/1‑139 (MQ=255)

                                                                                              cTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGAATTAGCATCCGtct                                      >  2:625119/1‑131 (MQ=255)

                                                                                                tACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca                            <  1:456905/139‑1 (MQ=255)

                                                                                                  ccTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcata                          <  2:386831/139‑3 (MQ=255)

                                                                                                        cAAAACCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGAtt                    <  1:894572/139‑1 (MQ=255)

                                                                                                          aaaCCAGTAAATATTGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTAc                  <  1:35274/139‑1 (MQ=255)

                                                                                                                       ttGCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGgtagta     <  1:837248/139‑1 (MQ=255)

                                                                                                                         gCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGca                                                                                    >  1:693432/1‑58 (MQ=255)

                                                                                                                         gCTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGca                                                                                    <  2:693432/58‑1 (MQ=255)

                                                                                                                          cTCGGGTAGCAAATTAC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAAca  >  1:115078/1‑139 (MQ=255)

TTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATTA‑‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACA  >  NC_000913/2484754‑2485013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A