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
A9 F59 I0 R1	41	42.9	928050	95.2%	883503	140.9

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%	105.2 / NA	34	V470D (GTT→GAT)	USA300HOU_1157	non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (19/15); total (19/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAA  >  CP000730/1233368‑1233634

ggTGAACGTGTTGAAGGTGGTGACAGTGTTGAGGTTGGTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACg                                                                                                                                <  1:441123/141‑1 (MQ=255)

 gTGAACGTGTTGAACGTGGTGACAGTTTTGATGTTGTTATATCAAAGGGCGCTGGAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTACAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGa                                                                                                                               <  2:335458/141‑1 (MQ=255)

   gAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGAtt                                                                                                                             <  1:167140/141‑1 (MQ=255)

     aCGTGTTGAACGTGGTGACAGTGTTGATGTGGTTATATCAAAGGGCCCGGAAAAGGTTAAAGTGCCAAATGTCCTTGGTTTACCTAAGGATGAAGCGTTGCAGAAATTAAAGTCGTTAGGTCTTAAAGATGATACGGTTGa                                                                                                                           >  2:302539/1‑141 (MQ=255)

        tgtTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTAATTGGTTTACCTAAGGAGGAAGACTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGaaaa                                                                                                                        >  1:352335/1‑141 (MQ=255)

             aaCGAGGTGACAATGATTATGTTGTTATATCAAAAGGCGCTGAAAAGGTCAAAATGCCAAATGTCAGTGGTTTACCTAAGGAAGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGtat                                                                                                                   <  2:142327/141‑1 (MQ=255)

                     gACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGCGGAAGCCTTGCAGAAATTAAAATCGTTGGGTCTTAAAGATGATACGATTGACAAAGTATATcataat                                                                                                           >  1:49594/1‑141 (MQ=255)

                            ttGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAgcgc                                                                                                    >  2:257179/1‑141 (MQ=255)

                                            aaaGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGc                                                                                    <  1:401366/141‑1 (MQ=255)

                                             aaGGACCCTGAAAAGGTTAAAGTGCCAAATGGCATTGGTGTACCTAAGGTGGAAGCCTTGCAGAAATTAAAATCGTTAGTTCTTAAAGAAAAAAAAAAAAAAAAAGTATAGAATAATCAAGCGCCAAAAGGATACAATGCa                                                                                   <  2:280971/141‑1 (MQ=255)

                                              aGGGCCCTGAAAAGGTTAAAATGCCAACTGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAGAAGTATAGAATAGTAAAGACCCAGAAGAAAAAATTCCaa                                                                                  >  2:383380/1‑141 (MQ=255)

                                              aGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCaa                                                                                  >  1:110060/1‑141 (MQ=255)

                                                ggCGCTGAAAAGGTTAAAATGCCGAATGTTATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTTATATCGTTATGTCTTAAAGATGATACGATTGTAAGAGATTATACTAATCAAGAGACAGAAGGATACATTGCaaga                                                                                >  2:22900/1‑139 (MQ=255)

                                                  cccTGAAAATGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAACGGATACATTGCAAATCa                                                                              >  1:338742/1‑141 (MQ=255)

                                                    cTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCaaa                                                                            >  2:145600/1‑141 (MQ=255)

                                                     ttaaaaGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGGTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAg                                                                           <  2:356752/139‑1 (MQ=255)

                                                     tGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCCAAAGAATACATTGCAAATCaaaa                                                                           >  2:72470/1‑140 (MQ=255)

                                                       aaaaGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAgtg                                                                         <  1:18314/141‑1 (MQ=255)

                                                        aaaGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAACTTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAgtgt                                                                        >  1:358882/1‑141 (MQ=255)

                                                              tAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAGAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGc                                                                  <  1:38417/141‑1 (MQ=255)

                                                                       aaaTGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATAAAGCGCTATTAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGa                                                         <  1:243143/141‑1 (MQ=255)

                                                                           gTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATc                                                     <  1:132903/141‑1 (MQ=255)

                                                                            tCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAACCGACAAATGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCg                                                    >  1:380348/1‑141 (MQ=255)

                                                                                      aCCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAGGTGTAACCGCAAATACTGAAATCGCTATTCATGa                                          >  1:91902/1‑141 (MQ=255)

                                                                                          aaGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCt                                      <  1:413897/141‑1 (MQ=255)

                                                                                              aggaAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTACAAATCAAAGTGTAACCGCAAATACTGAAAGCGCTATTCATGATTCTAata                                  <  2:91096/141‑1 (MQ=255)

                                                                                                 aaGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTa                               >  2:25322/1‑141 (MQ=255)

                                                                                                              aTTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGAATCTAATATTAAACTATATGaacc                  >  2:126570/1‑139 (MQ=255)

                                                                                                               ttAAAATCGTTAGGTCTTAAAGATGATACGATTGAACCAGTACATAAGAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCGATTCATGATTCTAATATTAAACTATATGAATCt                 >  1:435768/1‑141 (MQ=255)

                                                                                                                         tAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTa       >  1:188077/1‑141 (MQ=255)

                                                                                                                          aGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTaa      >  2:162903/1‑141 (MQ=255)

                                                                                                                            gTCTTAAAGATCATACGATTGAAAAAGTATATAATAAGCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGc    <  2:352335/141‑1 (MQ=255)

                                                                                                                             tCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCa   <  1:270771/141‑1 (MQ=255)

                                                                                                                              cTTAAAGATGATACGATTGAAAAAGTATATAGTAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGACATTAAGCaa  >  1:113878/1‑141 (MQ=255)

GGTGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAA  >  CP000730/1233368‑1233634

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A