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
A7 F123 I0 R1	46	52.8	1143652	95.1%	1087613	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,440,085	G→T	100%	intergenic (‑45/‑891)	cspA ← / → xpaC	cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,440,085	0	G	T	100.0%	133.5 / NA	42	intergenic (‑45/‑891)	cspA/xpaC	cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (24/18); total (24/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTA  >  CP000730/1439955‑1440213

tGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaa                                                                                                                        <  1:20949/141‑1 (MQ=255)

 gTAGGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATATGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATCTTACaaa                                                                                                                       >  1:410602/1‑141 (MQ=255)

         aCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATGATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACAt                                                                                                               >  2:378376/1‑141 (MQ=255)

         aCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATatct                                                                                                               >  2:281678/1‑138 (MQ=255)

            tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCa                                                                                                            <  1:178459/141‑1 (MQ=255)

                    tcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATCCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc                                                                                                    <  1:351186/141‑1 (MQ=255)

                        tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                <  1:320671/141‑1 (MQ=255)

                         caccTTCGATGAGCCCGAATCCTTTTTCATCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAATATCCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                                                               <  2:557860/138‑1 (MQ=255)

                                 aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCttt                                                                                       <  2:507392/141‑1 (MQ=255)

                                    aaGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCa                                                                                    >  2:524908/1‑141 (MQ=255)

                                     aGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCCTATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCaa                                                                                   >  2:128229/1‑141 (MQ=255)

                                      gCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACATCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGAAat                                                                                  >  2:497756/1‑141 (MQ=255)

                                        cGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                                <  1:232541/141‑1 (MQ=255)

                                           aTCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGa                                                                             >  2:350781/1‑141 (MQ=255)

                                                ttttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATCCGTTGCAATATGGaataat                                                                        <  2:123918/141‑1 (MQ=255)

                                                      gCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCTCTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                  <  2:375965/141‑1 (MQ=255)

                                                       cGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACCTGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGc                                                                 <  1:449813/141‑1 (MQ=255)

                                                       accaaaaCCATTTCAACATACCTTTCTTTCTAATCCAAAACCTCCAAGACTAAAATTCATTCAATACGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAGCCAAATATTCTTTGCAATATGGAATAATCATCTGc                                                                 <  2:211501/137‑1 (MQ=255)

                                                        gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt                                                                >  2:242927/1‑141 (MQ=255)

                                                            aaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCCAATTTCACTCAAATATTCTTTGCAATATGGAATAATCCTCTCCTTAAc                                                            >  1:158456/1‑141 (MQ=255)

                                                              ccATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACtt                                                          >  2:566044/1‑141 (MQ=255)

                                                              ccATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACtt                                                          <  1:314820/141‑1 (MQ=255)

                                                                 tttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATTTGGAATAATCATCTGCTTAACTTGta                                                       >  1:70935/1‑141 (MQ=255)

                                                                     aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                   >  1:166621/1‑141 (MQ=255)

                                                                     aCTGTACCTTGTTTCATAAACTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                   >  1:426114/1‑141 (MQ=255)

                                                                      cTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATtata                                                  <  1:71561/141‑1 (MQ=255)

                                                                        gTACCTTGTTTCATAATCTGAAACCTCCCAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGt                                                >  2:50604/1‑141 (MQ=255)

                                                                              tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                          <  1:505703/141‑1 (MQ=255)

                                                                              tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                          >  2:329140/1‑141 (MQ=255)

                                                                                 ttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatt                                       >  2:204568/1‑141 (MQ=255)

                                                                                   catatgcTGAATCCTCACAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAGTTCACTCAAATATGCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTAc                                     <  2:339429/135‑1 (MQ=255)

                                                                                     tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTGTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa                                   >  2:304009/1‑141 (MQ=255)

                                                                                     tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa                                   >  2:105040/1‑141 (MQ=255)

                                                                                     tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa                                   >  1:40107/1‑141 (MQ=255)

                                                                                        tCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAt                                <  1:352425/141‑1 (MQ=255)

                                                                                                     aGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACaataa                   >  2:197848/1‑141 (MQ=255)

                                                                                                     aGACTAAAATTCATGCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAACATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcattccattat                   >  2:389809/1‑132 (MQ=255)

                                                                                                          aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGTAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa              >  2:456891/1‑141 (MQ=255)

                                                                                                            aaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCCAATTGCAATACAATAATaaaaaa            >  1:82835/1‑141 (MQ=255)

                                                                                                               gaagacaAAATGCTTATTCTCATATAAAAAAAAAAAAATACAAATTTCACTCAAATATTCCGTGCAATATCGAATAAGCATCTGCTTAACTGGTATTATAGTGCAGTTATTACCAAATTGTAAAAAAAAAAAAAAAAatat         <  2:281607/136‑1 (MQ=255)

                                                                                                                     aaTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCAttt   <  1:524908/141‑1 (MQ=255)

                                                                                                                      atatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTa  >  2:524061/1‑141 (MQ=255)

TGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTA  >  CP000730/1439955‑1440213

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A