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
A4 F1 I2 R1	67	32.5	1435938	95.9%	1377064	112.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,401,304	T→C	S211S (TCT→TCC)	hflX →	GTPase, stimulated by 50S subunit binding, Mn(2+) homeostasis regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,401,304	0	T	C	88.2%	100.0 / 2.0	34	S211S (TCT→TCC)	hflX	GTPase, stimulated by 50S subunit binding, Mn(2+) homeostasis regulator
Reads supporting (aligned to +/- strand): ref base T (2/2); new base C (14/16); total (16/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

TAATCGCATCGTGCAGATACAGTCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCTACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGATGTCGGTGAAACCGTACTTGCAGATACCGTAGGGTT  >  NC_000913/4401175‑4401435

tAATCGCATCGTGCAGATACAGTCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTc                                                                                                                            <  2:652976/139‑1 (MQ=255)

       aTCGTGCAGATACAGTCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCa                                                                                                                     <  2:351632/139‑1 (MQ=255)

                     gTCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCgg                                                                                                       <  2:596710/139‑1 (MQ=255)

                      tCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAATTCCACCCTTTTCAATCg                                                                                                                       >  1:457371/1‑122 (MQ=255)

                      tCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAATTCCACCCTTTTCAATCg                                                                                                                       <  2:457371/122‑1 (MQ=255)

                      tCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCTACCCTTTTCAATCGCATCACCGAAgc                                                                                                           <  2:598221/134‑1 (MQ=255)

                      tCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCTACCCTTTTCAATCGCATCACCGAAgc                                                                                                           >  1:598221/1‑134 (MQ=255)

                       cgcgCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGt                                                                                                     <  2:262018/139‑1 (MQ=255)

                          gcCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTa                                                                                                  >  1:102795/1‑139 (MQ=255)

                                    agTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGAc                                                                                        >  1:58368/1‑139 (MQ=255)

                                     gTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGAcc                                                                                       <  1:469919/139‑1 (MQ=255)

                                         aaaaGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAgtt                                                                                   >  2:126733/1‑139 (MQ=255)

                                                          gggCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCgg                                                                                             >  2:566915/1‑112 (MQ=255)

                                                          gggCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCgg                                                                                             <  1:566915/112‑1 (MQ=255)

                                                               gcAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCTACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCgg                                                                                             >  2:536977/1‑107 (MQ=255)

                                                               gcAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCTACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCgg                                                                                             <  1:536977/107‑1 (MQ=255)

                                                                             aaGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGa                                               <  2:58368/139‑1 (MQ=255)

                                                                                 cGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGtt                                           <  1:126733/139‑1 (MQ=255)

                                                                                    cGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCa                                        >  1:416190/1‑139 (MQ=255)

                                                                                          tACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTgcg                                                        <  2:552944/117‑1 (MQ=255)

                                                                                          tACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTgcg                                                        >  1:552944/1‑117 (MQ=255)

                                                                                                 tCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGAt                                     <  2:5167/129‑1 (MQ=255)

                                                                                                 tCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGAt                                     >  1:5167/1‑129 (MQ=255)

                                                                                                 tCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGATGTCGGTGaaa                           <  2:416190/139‑1 (MQ=255)

                                                                                                 tCGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGATGTCGGTGaaa                           >  2:529842/1‑139 (MQ=255)

                                                                                                  cGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCa                                                                                                                     <  1:686741/48‑1 (MQ=255)

                                                                                                  cGCTGGTGGGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCa                                                                                                                     >  2:686741/1‑48 (MQ=255)

                                                                                                      ggtggGATATACCAACGCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGATGTCGGTGAAACCGTa                      <  1:529842/139‑1 (MQ=255)

                                                                                                                      gCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAgc                                                                                                           <  1:597417/38‑1 (MQ=255)

                                                                                                                      gCCGGTAAATCCACCCTTTTCAATCGCATCACCGAAgc                                                                                                           >  2:597417/1‑38 (MQ=255)

                                                                                                                         ggTAAATCCACCCTTTTCAATCGCATCACCGAAgcg                                                                                                          >  1:64406/1‑36 (MQ=255)

                                                                                                                         ggTAAATCCACCCTTTTCAATCGCATCACCGAAgcg                                                                                                          <  2:64406/36‑1 (MQ=255)

                                                                                                                          gTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGATGTCGGTGAAACCGTACTTGCAGATACCGTAGGGtt  >  1:557149/1‑139 (MQ=255)

                                                                                                                          gTAAATCCACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGATGTCGGTGAAACCGTACTTGCAGATACCGTAGGGtt  >  2:601194/1‑139 (MQ=255)

TAATCGCATCGTGCAGATACAGTCGCGCCTGGAAAGAGTTGAAAAGCAGCGTGAGCAGGGGCGGCAATCGCGTATCAAAGCCGACGTTCCTACTGTTTCGCTGGTGGGATATACCAACGCCGGTAAATCTACCCTTTTCAATCGCATCACCGAAGCGCGGGTCTACGCGGCAGACCAGTTGTTTGCCACCCTCGACCCGACGTTGCGGCGTATTGACGTTGCAGATGTCGGTGAAACCGTACTTGCAGATACCGTAGGGTT  >  NC_000913/4401175‑4401435

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A