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
A91 F1 I1 R1	18	55.4	3661525	95.1%	3482110	76.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	2,529,500	T→C	L63P (CTG→CCG)	hyfG →	hydrogenase 4, subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	2,529,500	0	T	C	96.3%	96.8 / ‑4.0	27	L63P (CTG→CCG)	hyfG	hydrogenase 4, subunit
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (11/15); total (11/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

TGAAAATCAATCTGCTGCCTGACGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCTGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTCAATGGAAGGGGCCG  >  REL606/2529431‑2529571

tGAAAATCAATCTGCTGCCTGACGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTgg                                                                   <  2:1325950/76‑1 (MQ=255)

 gAAAATCAATCTGCTGCCTGACGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGc                                                                  <  1:964193/76‑1 (MQ=255)

        aatcTGCTGCCTGACGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAacgacg                                                           <  1:1504446/76‑1 (MQ=255)

            tgctgcCTGACGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCg                                                       <  2:151853/76‑1 (MQ=255)

             gctgcCTGACGTTGTACATTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCgg                                                      <  1:1265754/76‑1 (MQ=255)

               tgcCTGGCGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGac                                                    <  1:1444388/76‑1 (MQ=255)

               tgcCTGACGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGac                                                    >  1:883077/1‑76 (MQ=255)

                  cTGACGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAAAGACGAGCGGACACt                                                 >  1:499645/1‑76 (MQ=255)

                       gTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACg                                            >  1:1260536/1‑76 (MQ=255)

                        ttGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACgg                                           >  2:798682/1‑76 (MQ=255)

                         tGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAAAggg                                          >  2:886284/1‑75 (MQ=255)

                           tACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCa                                        >  1:110936/1‑76 (MQ=255)

                            aCAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCAt                                       >  2:523763/1‑76 (MQ=255)

                             cAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGGCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCAtt                                      <  1:1158006/76‑1 (MQ=255)

                                tATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTAcg                                   <  1:1515332/76‑1 (MQ=255)

                                tATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTAcg                                   >  1:1688841/1‑76 (MQ=255)

                                   cTTTATTATCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCgg                                <  1:391484/76‑1 (MQ=255)

                                      tattatCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCACTACGCGGttt                             >  2:1276578/1‑76 (MQ=255)

                                        ttacCAACATGATGGCTGGCTTCCCGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTttat                           <  1:200816/76‑1 (MQ=255)

                                         tatCAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTttatt                          <  1:1500648/76‑1 (MQ=255)

                                          atCAACATGATGGCTGGCTTCCGGTCCTGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTttatta                         <  1:351153/76‑1 (MQ=255)

                                            cAACATGATGGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATg                       >  2:599096/1‑76 (MQ=255)

                                                  gatgGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCttt                 <  1:1112119/76‑1 (MQ=255)

                                                   atgGCTGGCTTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTc                >  1:700334/1‑76 (MQ=255)

                                                       ctggctTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTCAATg            <  1:1454718/76‑1 (MQ=255)

                                                           ctTCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTCAATGGAAg        <  2:1704316/76‑1 (MQ=255)

                                                            ttCCGGTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTCAATGGAAgg       <  1:293938/76‑1 (MQ=255)

                                                               cGGTCCCGTTTGGGAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTCAATGGAAGGGGc    <  2:1530323/76‑1 (MQ=255)

                                                                 gTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTCAATGGAAGGGGCCg  <  2:1249221/76‑1 (MQ=255)

                                                                 gTCCCGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTCAATGGAAGGGGCCg  <  1:271112/76‑1 (MQ=255)

TGAAAATCAATCTGCTGCCTGACGTTGTACAGTATCTTTATTATCAACATGATGGCTGGCTTCCGGTCCTGTTTGGCAACGACGAGCGGACACTTAACGGTCATTACGCGGTTTATTATGCCCTTTCAATGGAAGGGGCCG  >  REL606/2529431‑2529571

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A