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
A3 F17 I0 R1	155	84.1	1797446	90.9%	1633878	230.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	433,649	T→G	41.1%	G65G (GGT→GGG)	ribD →	fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	433,649	0	T	G	41.1%	3.2 / 3.5	26	G65G (GGT→GGG)	ribD	fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
Reads supporting (aligned to +/- strand): ref base T (5/10); new base G (9/2); total (14/12)
Fisher's exact test for biased strand distribution p-value = 2.14e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.31e-01

CAAAGAATTTGGCGAAGAGATCGCGCGCCTGGAGGACTAAGCCGTGCAGGACGAGTATTACATGGCGCGGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑GTGGACTTTACCGTCTGCAACAGGCTGGCATTGACGTCAGCCACGGCCTGATGATGAGTGAAGCCGAGCAATTGAATAAAGGCTTTCTCAAGC  >  NC_000913/433412‑433875

cAAAGAATTTGGCGAAGAGATCGCGCGCCTGGAGGACTAAGCCGTGCAGGACGAGTATTACATGGCGCGGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGGGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAGAAAACCAAA‑GGTg                                                                                                                                                                                                                                     >  2:199701/1‑239 (MQ=255)

       tttGGCGAAGAGATCGCGCGCCTGGAGGACTAAGCCGTGCAGGACGAGTATTACATGGCGCGGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGGGGAAAAGGCAAA‑GAGGCGAcca                                                                                                                                                                                                                               >  2:481588/1‑237 (MQ=255)

         tGGCGAAGAGATCGCGCGCCTGGAGGACTAAGCCGTGCAGGACGAGTATTACATGGCGCGGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACAACCAACGTGCGGGTGAACCACATGCCGAAGTACACCCGTTGCGTATGGCGGGGGAAAAAACCAAA‑AGGGCGAACCCCt                                                                                                                                                                                                                            >  2:542385/1‑239 (MQ=255)

                      gcgcgcCGGGAGGACTAAGCCGTGCAGGACGATTATTACATGGCGCGGGCGCTAAAGCGGGCGAAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑GGTGCGACCGCCTATGTCACACTCG‑a                                                                                                                                                                                                              <  2:342908/239‑1 (MQ=255)

                                 ggaCTAAGCCGTGCAGGACGAGTATTACATGGCGCGGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGACGGTGAAGGTTACCACCAACGTGCGGGGGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGGGAAAAAACCAAA‑GAGGCGCCCGCCCATGTCCCACCCG‑AAACCTTTAGc                                                                                                                                                                                                    >  2:436637/1‑238 (MQ=255)

                                                 gACGAGTATTACATGGCGCGGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGGGAAAAAGCCAAA‑GGGGGGACCCCCCATGTCACACCCC‑AACCCATGAACCACCATGGTCGTAccc                                                                                                                                                                                    >  2:155995/1‑236 (MQ=255)

                                                   cGAGTATTACATGGCGCGGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑AGTGCGACCGCCTCTGTCACACTCC‑AACCCTGTACCCAACATggggggacaccc                                                                                                                                                                                  >  2:510124/1‑228 (MQ=255)

                                                       tttttcatgggcggggCGCGACAGTGGGCGCACGGAGGTCTTTTTACCACGCCACCCACCCGGAAGGGGGGGGGCGTCAGTGTCAAAGATGGAGAAATTGGCGTGGAAGGTCCCCCCCAACGTGCGGGTGACCCACATGCCGAAGTACTCGCGTTGGGTATGGCGGGTGAAAAAGCCAAA‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTg                                                                                                                                                                             <  1:308867/226‑1 (MQ=255)

                                                                gcggGGGCGATAAAGGTGGCGCAACGAGGGCGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGGCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACg                                                                                                                                                                     <  2:114094/238‑1 (MQ=255)

                                                                 cgcgGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑AGGGCGACCGCCCATGTCAACATCG‑AACCCCGTAGCCATCATGGTCGTACGcccgtctcttataaaca                                                                                                                                                                    >  2:873970/1‑223 (MQ=255)

                                                                                                    aCCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTc                                                                                                                                >  2:624020/1‑239 (MQ=255)

                                                                                                      cACGCACCCCAACCCGAATGGGGGGTGAGTCATTGTCAAAGATGGCGAATTTGGCGGTGAAGGTTCCCCCCAACGTGGGGGTGAACCACATGCCGAAGTACCCGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGa                                                                                                                              <  2:204095/239‑1 (MQ=255)

                                                                                                                       aTGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGGGAAAAAGCCAAA‑GGGGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGGGCTGTGACGCACTCATCGCCGCCGGCGTAGCGCGCGGGGTTGCCTCGGTGCCAGAACCTAAccc                                                                                                              >  2:521867/1‑238 (MQ=255)

                                                                                                                             ggTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑AGGGCGAACCCCTAAGTCCAACCTG‑AACCCCGTAACCACAAAGGGCGTAACCCCCCCGGCTGTGACGCCCTCCTCCCCCCTGGCGTAGCGCGCCGGGTTGCTCCGATTCacaaaaccaaccccccagcc                                                                                                       >  1:673984/1‑220 (MQ=255)

                                                                                                                             ggTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGGGAAAAAGCCAAA‑GGGGCGGCCCCCCATGGCCCACCCGCAACCCT‑TAGCCAACATGGTCGTAAGCCCCCCTGCTCTGACGCACCCCTCACCGCTCGCCGAGCGCGCGCGGGTGTCTCCAGGCAAGAACCCAAcaccccgggc                                                                                                       >  1:38413/1‑230 (MQ=255)

                                                                                                                                    catggacgaagggggaaaaaTTGGCGGGGAAGGTTCCCACCAGGGGGGGGGGAAACCACAGGCCGAAGTACGCGCGTGGGTTAGGGGGGGTGAAAAAGCAAAA‑GGTGCGCCCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGc                                                                                                <  1:624020/222‑1 (MQ=255)

                                                                                                                                      tttacaagtgtggcaagttgtcaggTAAAGGTTCCCACCACCGGGCGGATAACCCACCGGCCGAATGCCACGCGTTGCGTATGGC‑GGTAAAAAAGTCAAAGGGTGCGCCCGCCTATGGCACACTCG‑AACCCTGTAGCCATCATGGACGTACGCCCCCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑Gt                                                                                             <  1:221065/216‑1 (MQ=255)

                                                                                                                                      ttGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGGGGGTGAACCACATGCCGAAGTACACGAGTTGGTTATGGCGGGTAAAAAAGCCAAG‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑Gt                                                                                             <  2:435841/239‑1 (MQ=255)

                                                                                                                                                                       accaccAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAACCAAA‑GGTGCGACCGCCCATGTCCCACTCG‑AACCCTGTAGCCATCATGGGCGTACGCCCCCGTGCTCGGTCGCACCCATCGCCCCCGGCGTAGCCCGCGGGGGTGCCTCCTTGCAAGATCCTAACCCGCCGGGCCCCGGGC‑GGGGGCTTTTCCGCCTGCAAAAAGCCGCCAtttg                                                             >  1:385754/1‑236 (MQ=255)

                                                                                                                                                                         ccacaacggcggggtaacccaagtGCAGAAGTACACGGTTTGCGTATGGGGGGTAAAAAAGCAAAA‑GGTGCCACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑GTGGACTTTACCGTCTGCAACAGGCTGGCATTGACGt                                                          <  2:533456/216‑1 (MQ=255)

                                                                                                                                                                              aCGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGGCGTACGCCCCCCTGCTGTGACGCACTCCTCGCCCCTGGCGTCGCGCGCGGGGTTGCCTGCCTGCAAAACCCCAACCCCCCGGGCGCTGGGCGGGGGGCTTTACC‑TCTGCAAAAgggcggccatgtcctacgcc                                                     >  1:533456/1‑221 (MQ=255)

                                                                                                                                                                               cgggggggacaaCCACAGGGCGAAGTACCCGTGTTGCGTAGGGGGGGAAAAAAACCCAAA‑GGGGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑GTGGACTTTACCGTCTGCAACAGGCTGGCATTGACGTCAGCCa                                                    <  2:385754/229‑1 (MQ=255)

                                                                                                                                                                                   cGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGGGAAAAAGCCAAA‑GGGGCCACCGCCTATGTCACACCCG‑AACCCTGTAGCCATCATGGTCGGACGCCACCGTGCTGTGACGCCCCCCTCCCCCCCCGCGTACGCCGCGGGGGTGCCTCGCTGCAAGCACCTAACCCCCCGGCCCCCGGGG‑GCGGGCTTTTCCGTCGCCAAAAGCCCGGCacttgcgtccaccccggc                                                >  1:834482/1‑222 (MQ=255)

                                                                                                                                                                                                      ggtcctcggtttggttgtGGGGGGTGAAAAACCAAAG‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGTGCGTACGCCACCGTGCTGTGACGCACTCCTCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑GTGGACTTTACCGTCTGCAACAGGCTGGCATTGACGTCAGCCACGGCCTGATGATGAGTGAAGCCg                             <  1:436637/222‑1 (MQ=255)

                                                                                                                                                                                                      agaccgcgggtggCGTATGGCGGGTAAAAAAGCCAAG‑GGGGCCACCGCCTATGTCCCCCTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑GTGGACTTTACCGTCTGCAACAGGCTGGCATTGACGTCAGCCACGGCCTGATGATGAGTGAAGCCg                             <  2:242532/227‑1 (MQ=255)

                                                                                                                                                                                                                                 aaagGCCAAG‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGGGCTGTGACGCACTCAGCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑GTGGACTTTACCGTCTGCAACAGGCTGGCATTGACGTCAGCCACGGCCTGATGATGAGTGAAGCCGAGCAATTGAATAAAGGCTTTCTCAAGc  <  2:834482/239‑1 (MQ=255)

CAAAGAATTTGGCGAAGAGATCGCGCGCCTGGAGGACTAAGCCGTGCAGGACGAGTATTACATGGCGCGGGCGCTAAAGCTGGCGCAACGAGGACGTTTTACCACGCATCCCAACCCGAATGTCGGGTGCGTCATTGTCAAAGATGGCGAAATTGTCGGTGAAGGTTACCACCAACGTGCGGGTGAACCACATGCCGAAGTACACGCGTTGCGTATGGCGGGTGAAAAAGCCAAA‑GGTGCGACCGCCTATGTCACACTCG‑AACCCTGTAGCCATCATGGTCGTACGCCACCGTGCTGTGACGCACTCATCGCCGCTGGCGTAGCGCGCGTGGTTGCCTCGATGCAAGATCCTAACCCGCAGGTCGCTGGGC‑GTGGACTTTACCGTCTGCAACAGGCTGGCATTGACGTCAGCCACGGCCTGATGATGAGTGAAGCCGAGCAATTGAATAAAGGCTTTCTCAAGC  >  NC_000913/433412‑433875

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A