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
A13 F1 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,765,829	(C)_5→4	intergenic (‑53/‑89)	yfjM ← / → rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,765,825	0	C	.	100.0%	198.6 / NA	49	intergenic (‑49/‑93)	yfjM/rnlA	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (24/25); total (24/25)

AAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGG  >  NC_000913/2765711‑2765957

aaGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                              <  1:626419/139‑1 (MQ=255)

aaGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                              <  1:1587090/139‑1 (MQ=255)

     tCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         >  1:1159213/1‑139 (MQ=255)

             ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAgg                                                                                                                           <  2:420246/113‑1 (MQ=255)

             ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAgg                                                                                                                           >  1:420246/1‑113 (MQ=255)

             ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         >  2:511609/1‑131 (MQ=255)

             ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         <  1:511609/131‑1 (MQ=255)

                  tGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAg                                                                                            <  1:1378600/139‑1 (MQ=255)

                    gTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGCACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                                                          <  1:530107/139‑1 (MQ=255)

                        gaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         <  2:1280351/120‑1 (MQ=255)

                        gaTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         >  1:1280351/1‑120 (MQ=255)

                         aTCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGta                                                                                     <  2:1159213/139‑1 (MQ=255)

                                   ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTaga                                                                           >  2:1012964/1‑139 (MQ=255)

                                   ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATAAACTTCAAGGGGGTATTATTGTaga                                                                           >  1:695197/1‑139 (MQ=255)

                                      tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                                                              >  2:934151/1‑101 (MQ=255)

                                      tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTAGCTAAATTCAg                                                                                                              <  1:934151/101‑1 (MQ=255)

                                             aCGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCat                                                                 <  2:695197/139‑1 (MQ=255)

                                                   gACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                       <  1:723568/111‑1 (MQ=255)

                                                   gACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                       >  2:723568/1‑111 (MQ=255)

                                                               cATTTTGTGGACTGCCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATcc                                               >  2:882395/1‑139 (MQ=255)

                                                               cATTTTGTGGACTGCCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATcc                                               >  2:267807/1‑139 (MQ=255)

                                                                 ttttGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                    <  1:15523/84‑1 (MQ=255)

                                                                 ttttGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                    >  2:15523/1‑84 (MQ=255)

                                                                     gtgGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                       <  2:258823/93‑1 (MQ=255)

                                                                     gtgGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                                                       >  1:258823/1‑93 (MQ=255)

                                                                           tG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTa                                                                             <  2:1120203/97‑1 (MQ=255)

                                                                           tG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTa                                                                             >  1:1120203/1‑97 (MQ=255)

                                                                            g‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATg                                                     >  1:975393/1‑119 (MQ=255)

                                                                            g‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATg                                                     <  2:975393/119‑1 (MQ=255)

                                                                              cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                    >  1:1555519/1‑72 (MQ=255)

                                                                              cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                    <  2:1555519/72‑1 (MQ=255)

                                                                              cccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCC‑GGAAATGACAATCAg                               >  2:220903/1‑139 (MQ=255)

                                                                               ccccccGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCCAGGAAATGACAATCAg                               <  1:1164382/139‑1 (MQ=255)

                                                                                              tCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAACACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATc                                                >  2:424017/1‑107 (MQ=255)

                                                                                              tCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAACACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATc                                                <  1:424017/107‑1 (MQ=255)

                                                                                                 tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         >  2:458209/1‑48 (MQ=255)

                                                                                                 tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         <  1:458209/48‑1 (MQ=255)

                                                                                                 tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTaaa             >  1:745843/1‑139 (MQ=255)

                                                                                                 tGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCGAAATTTAGCAAATCTATACACTTCAGTGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTaaa             >  1:1041348/1‑139 (MQ=255)

                                                                                                  gCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAAt            <  1:882395/139‑1 (MQ=255)

                                                                                                  gCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAAt            <  1:267807/139‑1 (MQ=255)

                                                                                                       ataGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGt       <  1:1279556/139‑1 (MQ=255)

                                                                                                        taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         <  2:457958/41‑1 (MQ=255)

                                                                                                        taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                                                         >  1:457958/1‑41 (MQ=255)

                                                                                                        taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                    >  2:231327/1‑46 (MQ=255)

                                                                                                        taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                    <  2:1083478/46‑1 (MQ=255)

                                                                                                        taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                    <  1:231327/46‑1 (MQ=255)

                                                                                                        taGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                                                                    >  1:1083478/1‑46 (MQ=255)

                                                                                                             ggAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAggg  >  1:1240503/1‑139 (MQ=255)

AAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATAT‑GTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGG  >  NC_000913/2765711‑2765957

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A