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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,443,964	A→G	D528G (GAT→GGT)	tamA →	translocation and assembly module for autotransporter export, outer membrane subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,443,964	0	A	G	96.9%	108.1 / ‑3.8	32	D528G (GAT→GGT)	tamA	translocation and assembly module for autotransporter export, outer membrane subunit
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (19/12); total (19/13)
Fisher's exact test for biased strand distribution p-value = 4.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

ACAAATACAAATCTATCGCTCCGAAATACGCCAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGATATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACATCGGTCTGGGGCC  >  NC_000913/4443817‑4444105

acaaatacaaatCTATCGCTCCGAAATACGCCAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGgtat                                                                                                                                            >  1:165481/1‑151 (MQ=255)

         aatCTATCGCTCCGAAATACGCCAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTcgccgc                                                                                                                                     >  2:59406/1‑149 (MQ=255)

         aatCTATCGCTCCGAAATACGCCAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTcgccg                                                                                                                                      >  1:298616/1‑148 (MQ=255)

              aTCGCTCCGAAATACGCCAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGAc                                                                                                                               <  1:109155/150‑1 (MQ=255)

                 gCTCCGAAATACGCCAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTa                                                                                                                           <  1:446399/151‑1 (MQ=255)

                        aaTACGCCAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCgg                                                                                                                    <  1:584825/151‑1 (MQ=255)

                              ccAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCgg                                                                                                              >  2:126923/1‑151 (MQ=255)

                                         cTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTgc                                                                                                   >  1:614167/1‑151 (MQ=255)

                                                   ccTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATc                                                                                         <  1:126926/151‑1 (MQ=255)

                                                      cGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGcc                                                                                      >  2:468338/1‑151 (MQ=255)

                                                       gAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCg                                                                                     >  2:243499/1‑151 (MQ=255)

                                                          gTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTc                                                                                  >  2:171426/1‑151 (MQ=255)

                                                            tGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCgg                                                                                >  1:442258/1‑151 (MQ=255)

                                                              aTAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGc                                                                              >  2:257739/1‑151 (MQ=255)

                                                                        cGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACt                                                                    <  2:197443/151‑1 (MQ=255)

                                                                           tGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCg                                                                  >  2:342464/1‑150 (MQ=255)

                                                                                 aCCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGc                                                           >  2:446012/1‑151 (MQ=255)

                                                                                    aGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGt                                                        <  1:59406/151‑1 (MQ=255)

                                                                                    aGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGt                                                        <  2:104901/151‑1 (MQ=255)

                                                                                      tACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTAc                                                      >  2:90418/1‑151 (MQ=255)

                                                                                          aCGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCgg                                                   >  2:340920/1‑150 (MQ=255)

                                                                                                  ggAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGAt                                           >  1:503999/1‑150 (MQ=255)

                                                                                                      aaTGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATaa                                         >  2:344838/1‑148 (MQ=255)

                                                                                                      aaTGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGa                                      <  2:614150/151‑1 (MQ=255)

                                                                                                                       tttGTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGt                     >  2:59948/1‑151 (MQ=255)

                                                                                                                          gTCGATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGtttt                  <  1:497947/151‑1 (MQ=255)

                                                                                                                             gATAGTGGCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACa               <  1:263637/151‑1 (MQ=255)

                                                                                                                                   ggCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACATCGGTc         >  2:528655/1‑151 (MQ=255)

                                                                                                                                    gCGAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACATCGGTCt        <  1:207797/151‑1 (MQ=255)

                                                                                                                                      gAAGCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACATCGGTCTgg      >  1:524613/1‑151 (MQ=255)

                                                                                                                                         gCGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACATCGGTCTGGGGc   <  2:442250/151‑1 (MQ=255)

                                                                                                                                         gCGGTAAGCGATATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACATCGGTCTGGGGc   <  2:74980/151‑1 (MQ=255)

                                                                                                                                          cGGTAAGCGGTATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACATCGGTCTGGGGcc  >  1:135978/1‑151 (MQ=255)

ACAAATACAAATCTATCGCTCCGAAATACGCCAACGGTGACCTGAAAGGGGCCTCGAAGTTGATAACCGGATCGCTGGAATACCAGTACAACGTGACCGGAAAATGGTGGGGCGCGGTGTTTGTCGATAGTGGCGAAGCGGTAAGCGATATTCGCCGCAGCGACTTTAAAACCGGTACCGGGGTCGGCGTGCGCTGGGAATCGCCGGTCGGGCCAATCAAACTCGATTTTGCCGTACCGGTCGCGGATAAAGACGAACACGGGTTACAGTTTTACATCGGTCTGGGGCC  >  NC_000913/4443817‑4444105

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A