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
A17 F172 I1 R2	29	34.5	745914	96.0%	716077	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,679,710	G→T	G65V (GGC→GTC)	cbpD →	possible secretory antigen

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,679,710	0	G	T	96.3%	79.5 / ‑2.6	27	G65V (GGC→GTC)	cbpD	possible secretory antigen
Reads supporting (aligned to +/- strand): ref base G (1/0); new base T (14/12); total (15/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

CAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAA  >  CP000730/2679575‑2679843

cagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATg                                                                                                                                  >  1:323754/1‑141 (MQ=255)

cagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATg                                                                                                                                  <  2:316557/141‑1 (MQ=255)

          ttATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTg                                                                                                                        <  1:135199/141‑1 (MQ=255)

                aTCCGGCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTa                                                                                                                  <  2:300831/141‑1 (MQ=255)

                  ccGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACa                                                                                                                >  2:26781/1‑141 (MQ=255)

                   cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACaa                                                                                                               >  1:299323/1‑141 (MQ=255)

                         aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACg                                                                                                         >  1:189880/1‑141 (MQ=255)

                             aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTaaa                                                                                                     >  1:46760/1‑141 (MQ=255)

                                cATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATCGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCa                                                                                                  >  2:326762/1‑141 (MQ=255)

                                     aTCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAata                                                                                             >  2:266671/1‑141 (MQ=255)

                                            gCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACt                                                                                      >  1:350563/1‑141 (MQ=255)

                                              cGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTgg                                                                                    >  1:193764/1‑141 (MQ=255)

                                                    tAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTac                                                                              <  2:323754/141‑1 (MQ=255)

                                                         attatAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCaa                                                                         <  2:202572/141‑1 (MQ=255)

                                                                        aaTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTcc                                                          >  1:82/1‑140 (MQ=255)

                                                                                tggtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                                  >  1:329420/1‑141 (MQ=255)

                                                                                   tggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACt                                               >  1:287775/1‑141 (MQ=255)

                                                                                      gcttttAAACGCCGCGCACCAGTCAGTAAACCTGTTTCTAATAGATAGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCa                                            <  2:294145/138‑1 (MQ=255)

                                                                                            aaactacgcgCACAAGTCGGGAAACCTGTTTCTAATAGATGCATAAATGCTAAAAATTGCTATCACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGAATTCAACTGCAGGatat                                      <  2:159170/135‑1 (MQ=255)

                                                                                              aCGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGAtatta                                    <  2:1898/141‑1 (MQ=255)

                                                                                                       acaAGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGt                           <  1:92829/141‑1 (MQ=255)

                                                                                                          aGTCGGTAAACCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGc                        >  1:191715/1‑141 (MQ=255)

                                                                                                                  aaCCTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGttgttg                <  1:26781/141‑1 (MQ=255)

                                                                                                                    ccTGTTTCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATgcaaattgataaatc              >  1:369589/1‑127 (MQ=255)

                                                                                                                        tttCTAATAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAg          >  2:317896/1‑141 (MQ=255)

                                                                                                                              aTAGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTTGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGtatata    <  1:266671/141‑1 (MQ=255)

                                                                                                                                aGATGGGTCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATaaa  <  2:274758/141‑1 (MQ=255)

CAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAA  >  CP000730/2679575‑2679843

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

GATK/CNVnator alignment

N/A