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 I1 R1	86	24.1	1002126	98.1%	983085	121.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,684,038	G→A	G386D (GGC→GAC)	rstB →	sensory histidine kinase of RstAB two‑component system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,684,038	0	G	A	100.0%	139.0 / NA	40	G386D (GGC→GAC)	rstB	sensory histidine kinase of RstAB two‑component system
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (21/19); total (21/19)

CCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATT  >  NC_000913/1683907‑1684170

ccTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCggg                                                                                                                               >  1:395597/1‑139 (MQ=255)

    cTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCgggctgg                                                                                                                           >  2:15330/1‑139 (MQ=255)

                  tAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTc                                                                                                             <  2:495704/139‑1 (MQ=255)

                  tAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTc                                                                                                             <  2:249295/139‑1 (MQ=255)

                    gagCGACATTAATTGTTGGGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTAGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTTGGGCTGGCAATTGTCCa                                                                                                           <  1:233222/139‑1 (MQ=255)

                    gagCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCa                                                                                                           <  2:337979/139‑1 (MQ=255)

                    gagCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCa                                                                                                           <  1:35991/139‑1 (MQ=255)

                     agCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCAc                                                                                                          >  2:325274/1‑139 (MQ=255)

                              aaTTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCa                                                                                                 <  2:395597/139‑1 (MQ=255)

                                     gAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCa                                                                                                           <  2:473414/122‑1 (MQ=255)

                                     gAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCa                                                                                                           >  1:473414/1‑122 (MQ=255)

                                         atgatgGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATggg                                                                                      >  1:452224/1‑139 (MQ=255)

                                             tgGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCa                                                                                                 <  1:38640/124‑1 (MQ=255)

                                             tgGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCa                                                                                                 >  2:38640/1‑124 (MQ=255)

                                                cccAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCa                                                                                                           >  1:304989/1‑111 (MQ=255)

                                                cccAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCa                                                                                                           <  2:304989/111‑1 (MQ=255)

                                                  cAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGt                                                                             >  1:56991/1‑139 (MQ=255)

                                                    gggATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTa                                                                           <  1:397506/139‑1 (MQ=255)

                                                    gggATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTa                                                                           <  1:298652/139‑1 (MQ=255)

                                                         tGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGTGACTGCGGGCTGGGGCTGGCAATTGTc                                                                                                             <  2:324385/100‑1 (MQ=255)

                                                         tGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATtgt                                                                      >  2:263557/1‑139 (MQ=255)

                                                         tGCCCCAGAAAACCGCGAACATATCTTTGAACCTCTTGTTCGCCTCGATACCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTc                                                                                                             >  1:324385/1‑100 (MQ=255)

                                                          gCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCa                                                                                                                   >  1:33854/1‑93 (MQ=255)

                                                          gCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCa                                                                                                                   <  2:33854/93‑1 (MQ=255)

                                                           ccccAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCtat                                                                                                     <  2:166097/106‑1 (MQ=255)

                                                           ccccAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCtat                                                                                                     >  1:166097/1‑106 (MQ=255)

                                                                      cgcgAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGCGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAAc                                                         >  1:354004/1‑139 (MQ=255)

                                                                           aCATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGggt                                                    >  2:253974/1‑139 (MQ=255)

                                                                                     gAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCt                                          <  1:270036/139‑1 (MQ=255)

                                                                                       aCCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTtc                                        >  2:111938/1‑139 (MQ=255)

                                                                                                              gCCGGGATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCa                 <  1:253974/139‑1 (MQ=255)

                                                                                                                  ggATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTgg                            >  1:347107/1‑124 (MQ=255)

                                                                                                                  ggATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTgg                            <  2:347107/124‑1 (MQ=255)

                                                                                                                   gATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTc                                                                                                             >  2:471298/1‑42 (MQ=255)

                                                                                                                   gATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTc                                                                                                             <  1:471298/42‑1 (MQ=255)

                                                                                                                   gATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCgg                                                                                   <  2:182597/68‑1 (MQ=255)

                                                                                                                   gATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCgg                                                                                   >  1:182597/1‑68 (MQ=255)

                                                                                                                   gATCGCTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACa            >  2:66295/1‑139 (MQ=255)

                                                                                                                        cTCAACCGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCg       >  1:149388/1‑139 (MQ=255)

                                                                                                                             ccGGCGACTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAAtt  >  1:130650/1‑139 (MQ=255)

CCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGTTCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATGGCATAACATCCCGCAATT  >  NC_000913/1683907‑1684170

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A