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
A1 F104 I0 R1	106	58.2	1336546	90.2%	1205564	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,233,504	T→A	100%	V470D (GTT→GAT)	USA300HOU_1157 →	non‑specific serine/threonine protein kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,233,504	0	T	A	100.0%	171.3 / NA	55	V470D (GTT→GAT)	USA300HOU_1157	non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (27/28); total (27/28)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGTT  >  CP000730/1233372‑1233637

aaCGTGTTGAACGTGGTGACAGTGTTGATGTTGTTAGATCAAAGCGACACGACCACCTAGAAATTCCATATGTCAATGGTTGACTTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTAAAAGATGATACGATTg                                                                                                                               >  2:140997/1‑141 (MQ=255)

 aCGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGa                                                                                                                              <  2:340716/141‑1 (MQ=255)

      ttGAACGGGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAg                                                                                                                         <  2:632828/141‑1 (MQ=255)

              ggtgACAGTGTTGATGATGTTATATCAAAGGGCCCTGAGAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATataat                                                                                                                 >  1:371133/1‑141 (MQ=255)

                 gACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTAATTGGTGTACCTAAGGAGGACGCCTTGCCGAATTCAAAATCGTTAGGTCTGAAAGATGATACGATTGAAAAAGTATATaataat                                                                                                              >  2:140451/1‑141 (MQ=255)

                   cAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCa                                                                                                            >  1:242224/1‑141 (MQ=255)

                         ttaTGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCATAAATTAAAATCGTTAGGTTTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGcc                                                                                                      <  1:140997/139‑1 (MQ=255)

                         tGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGcc                                                                                                      >  1:562158/1‑141 (MQ=255)

                          gATGTTGTTATATCCAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCa                                                                                                     <  2:310488/141‑1 (MQ=255)

                             gttgttATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCaaaa                                                                                                  >  1:38656/1‑141 (MQ=255)

                              ttgttATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAg                                                                                                 <  1:306968/141‑1 (MQ=255)

                              ttgttATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAg                                                                                                 >  2:284064/1‑141 (MQ=255)

                              ttgttATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGCCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAACAg                                                                                                 <  2:189976/141‑1 (MQ=255)

                                       cAAAGGGCCCTGAAAAGGTTAAAATGGCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTg                                                                                        <  1:406771/141‑1 (MQ=255)

                                               ccTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATCTATTAATCAAGCGCCAAAAGGATACATTGCAAATCaa                                                                                >  1:297254/1‑141 (MQ=255)

                                               ccTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTACAAAGCaa                                                                                >  2:520826/1‑141 (MQ=255)

                                                cTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCaaa                                                                               >  1:343898/1‑141 (MQ=255)

                                                 tGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTCTATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAg                                                                              <  2:437577/141‑1 (MQ=255)

                                                 tGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAg                                                                              >  1:164030/1‑141 (MQ=255)

                                                    aaaGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAgtgt                                                                           <  1:466168/141‑1 (MQ=255)

                                                       ggTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTGAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAAc                                                                        >  1:477829/1‑141 (MQ=255)

                                                             aaTGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCaaa                                                                  <  1:644950/141‑1 (MQ=255)

                                                              aTGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGGAGAAGGTAAAATCGTTATGTCTTCAATATGATACGATTGAAAAAGTATATAATAATCACGCGCCAATAGGATACCTTGCATAGCAAAGTGTAACCGCAAAt                                                                 <  2:242224/141‑1 (MQ=255)

                                                              aTGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCaaaa                                                                 >  2:231132/1‑140 (MQ=255)

                                                                gCCAAATGTCATTGGTTTACCTAATGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATACTCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATAc                                                               <  1:499391/141‑1 (MQ=255)

                                                                 ccAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACt                                                              >  1:71188/1‑141 (MQ=255)

                                                                  cAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAGCCGCAAATACTg                                                             >  2:373178/1‑141 (MQ=255)

                                                                  cAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTg                                                             >  1:545764/1‑141 (MQ=255)

                                                                  cAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCAATTTCATAATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTg                                                             <  1:316257/141‑1 (MQ=255)

                                                                      tGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAAt                                                         >  1:406750/1‑141 (MQ=255)

                                                                         cATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGCAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCCAATACTGAAATCGc                                                      >  2:202138/1‑141 (MQ=255)

                                                                            tGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAATTACTGAAATCGCTAt                                                   <  1:495867/141‑1 (MQ=255)

                                                                            tGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTAt                                                   <  2:343898/141‑1 (MQ=255)

                                                                             ggTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGGCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAACTGTANCCGCAAATACTGAAATCGCTAtt                                                  >  1:377329/1‑141 (MQ=255)

                                                                                   ccTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGAt                                            >  1:6805/1‑141 (MQ=255)

                                                                                   ccTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCGTAAAGATGATACGACTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGGAAATCAAATTGTAACCGCAAGTACTGAAATCGCTGTTCATGAt                                            >  2:273830/1‑141 (MQ=255)

                                                                                    cTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGAtt                                           <  1:521441/141‑1 (MQ=255)

                                                                                      aaGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAATAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGCAATCGCTATTCATGATTCt                                         <  1:400040/141‑1 (MQ=255)

                                                                                      aaGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCt                                         <  1:243191/141‑1 (MQ=255)

                                                                                         gaggaAGCCTTGCAGAAATTAAAATCGTTCGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAat                                      <  1:236628/141‑1 (MQ=255)

                                                                                         gaggaAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAat                                      <  1:541641/141‑1 (MQ=255)

                                                                                            gaAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTCATAtt                                   >  2:580915/1‑141 (MQ=255)

                                                                                                   tGCATAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACtat                            <  2:154471/141‑1 (MQ=255)

                                                                                                    gCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACtata                           <  2:388846/141‑1 (MQ=255)

                                                                                                    gCAGAAATTAAAATCGTTAGGTCTCAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACtata                           <  1:636951/141‑1 (MQ=255)

                                                                                                     cAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTCTATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTATAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTatat                          >  2:435040/1‑141 (MQ=255)

                                                                                                             aaaaTCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCttt                  <  2:38656/141‑1 (MQ=255)

                                                                                                                     tAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTa          >  1:239846/1‑141 (MQ=255)

                                                                                                                     tAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTa          <  1:245948/141‑1 (MQ=255)

                                                                                                                      aGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGCTTCTAATATTAAACTATATGAGTCTTTAGGCATTaa         >  2:51224/1‑141 (MQ=255)

                                                                                                                       ggTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAg        <  2:538576/141‑1 (MQ=255)

                                                                                                                       ggTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTAAGGCATGAAg        <  2:407814/141‑1 (MQ=255)

                                                                                                                       ggTCTTAAAGATGATACGAATGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAg        <  2:407759/141‑1 (MQ=255)

                                                                                                                             aaaGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGtt  >  1:499475/1‑141 (MQ=255)

                                                                                                                             aaaGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGtt  >  1:115343/1‑141 (MQ=255)

AACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGTT  >  CP000730/1233372‑1233637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A