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	3,372,254	G→A	G107G (GGC→GGT)	nanT ←	sialic acid transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,372,254	0	G	A	93.9%	95.4 / 1.9	33	G107G (GGC→GGT)	nanT	sialic acid transporter
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (17/14); minor base C (1/1); total (18/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.69e-01

TGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AGCCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATAGCGCCGAGCATCAGGCCGCCGAACCAGCGA  >  NC_000913/3372122‑3372374

tGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGgc                                                                                                                    >  1:1358277/1‑139 (MQ=255)

               aCTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGcc                                                                                                     <  2:567686/139‑1 (MQ=255)

                   gCTTTGTTACGCAGATGTGTTGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCg                                                                                                 >  1:895675/1‑139 (MQ=255)

                        gTTACGCAGATGTTTTGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCg                                                                                            >  2:113037/1‑139 (MQ=255)

                           aCGCAGATGTTTTGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGcc                                                                                         <  1:907357/139‑1 (MQ=255)

                                      ttGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTg                                                                                                                      >  1:1308432/1‑99 (MQ=255)

                                      ttGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTg                                                                                                                      <  2:1308432/99‑1 (MQ=255)

                                           cAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCg                                                                                                           <  2:137806/105‑1 (MQ=255)

                                           cAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCg                                                                                                           >  1:137806/1‑105 (MQ=255)

                                           cAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATg                                                                          >  2:81127/1‑138 (MQ=255)

                                           cAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATg                                                                          <  1:81127/138‑1 (MQ=255)

                                              cTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCaa                                                                                                                >  1:309645/1‑97 (MQ=255)

                                              cTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCaa                                                                                                                <  2:309645/97‑1 (MQ=255)

                                              cTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTgg                                                                      >  1:650482/1‑139 (MQ=255)

                                                  cAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGACAAGAGAACGATGCTGGTGAc                                                                  <  2:895675/139‑1 (MQ=255)

                                                               ggCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAgacga                                                     >  2:523085/1‑139 (MQ=255)

                                                               ggCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAgacga                                                     >  2:1485558/1‑139 (MQ=255)

                                                                  gcTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGc                                                  >  1:753662/1‑139 (MQ=255)

                                                                   cTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGTAACCCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGAc                                                                  >  2:542235/1‑123 (MQ=255)

                                                                   cTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGTAACCCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGAc                                                                  <  1:542235/123‑1 (MQ=255)

                                                                              ttCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATTCTGGTGACCATTGCCAGACGACGc                                                  <  2:1069683/127‑1 (MQ=255)

                                                                              ttCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGc                                                  >  1:1069683/1‑127 (MQ=255)

                                                                                    cGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATa                                <  2:650482/139‑1 (MQ=255)

                                                                                      ccATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTg                                                                       <  2:1182580/98‑1 (MQ=255)

                                                                                      ccATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTg                                                                       >  1:1182580/1‑98 (MQ=255)

                                                                                      ccATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATAgc                              >  1:70044/1‑139 (MQ=255)

                                                                                         tCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATAGCGcc                           <  2:753662/139‑1 (MQ=255)

                                                                                                         cAGACGAGCGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATAGCGCCGAGCATCAGGccgccg           >  1:648435/1‑139 (MQ=255)

                                                                                                                 cGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCgagaagagaa                                                                               >  1:835631/1‑63 (MQ=255)

                                                                                                                 cGATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCgagaagagaa                                                                               <  2:835631/63‑1 (MQ=255)

                                                                                                                  gATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAg                                            <  2:1384525/97‑1 (MQ=255)

                                                                                                                  gATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAg                                            >  1:1384525/1‑97 (MQ=255)

                                                                                                                  gATAAACATGGTGATGT‑AACCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATAGCGCCGAGCATCAGGCCGCCGAACCAGCga  <  2:1358277/139‑1 (MQ=255)

TGAAATCAAAAAACCACTGGCTTTGTTACGCAGATGTTTTGGCCAGCTTTCAATGACATAGGTGGCGCTGGAACCGTATTCACCCGCCATCCCCATGCCGATGACCAGACGAGCGATAAACATGGTGATGT‑AGCCTGGCGCAAAGCCGCAGGCCAGCGTCCCGGCCGAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATAGCGCCGAGCATCAGGCCGCCGAACCAGCGA  >  NC_000913/3372122‑3372374

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A